starting phase `set-SOURCE-DATE-EPOCH'
phase `set-SOURCE-DATE-EPOCH' succeeded after 0.0 seconds
starting phase `set-paths'
environment variable `PATH' set to `/gnu/store/l1xmcy7vkq9bzvcx57zc9lyqyhy4qn7b-icedtea-3.19.0-jdk/bin:/gnu/store/dw5xn0v0ngz49gwlnrxrai9qdd80h021-ant-1.9.15/bin:/gnu/store/gfd1415b6lbhkp4kcqjapram7b4j7mbp-zip-3.0/bin:/gnu/store/hqysqhh80g7qy8287b8p2gwz0379vh50-tar-1.34/bin:/gnu/store/8rvnivj15gmirawhikgbjaang5b4w779-gzip-1.10/bin:/gnu/store/64zk0izmaframq6cd0xlsmk0rxn3zc52-bzip2-1.0.8/bin:/gnu/store/z6bw81zw5b5jm3p02y906p0wnjbjqa7n-xz-5.2.5/bin:/gnu/store/jfmrxybjkd0nvh1n34hbzv0lwsnmxz1v-file-5.39/bin:/gnu/store/49j4cjqc8sckyh4qhf9j9dmc6anc8wk9-diffutils-3.8/bin:/gnu/store/znjj5y98lvi46fll85qg22ngz966gx1d-patch-2.7.6/bin:/gnu/store/yq3xalg1p2p5p5hfpw4v5jx0v86qw45w-findutils-4.8.0/bin:/gnu/store/bgyr8c7bl1sqhpapm2kghiya0k6zvi51-gawk-5.1.0/bin:/gnu/store/dsldg7i4y6hxdknh7cv93rbxbp17xm93-sed-4.8/bin:/gnu/store/4znchc8whjbs50mvxgc0skmkvyhy9xk1-grep-3.6/bin:/gnu/store/wllq3y3sl5bldm9vsx2fcwhcmks4i9ar-coreutils-8.32/bin:/gnu/store/zyhbjfyqh10yiw1dw1x1i7n70jm9ygdn-make-4.3/bin:/gnu/store/2an4h5ndc22dv62q3l985ciq862q4bj7-bash-minimal-5.1.8/bin:/gnu/store/g58zxpycy64m790vwjlzpadmbn065fia-ld-wrapper-0/bin:/gnu/store/cr38d3gvf52ckns2b01lwgw86hk3mvcc-binutils-2.37/bin:/gnu/store/h88kd46c8br0wc4i6hq19cjby081ina4-gcc-10.3.0/bin:/gnu/store/mjdjgiz9k5rrbj440r16z6p5g33nr7d7-glibc-2.33/bin:/gnu/store/mjdjgiz9k5rrbj440r16z6p5g33nr7d7-glibc-2.33/sbin'
environment variable `BASH_LOADABLES_PATH' unset
environment variable `C_INCLUDE_PATH' set to `/gnu/store/l1xmcy7vkq9bzvcx57zc9lyqyhy4qn7b-icedtea-3.19.0-jdk/include:/gnu/store/64zk0izmaframq6cd0xlsmk0rxn3zc52-bzip2-1.0.8/include:/gnu/store/z6bw81zw5b5jm3p02y906p0wnjbjqa7n-xz-5.2.5/include:/gnu/store/jfmrxybjkd0nvh1n34hbzv0lwsnmxz1v-file-5.39/include:/gnu/store/bgyr8c7bl1sqhpapm2kghiya0k6zvi51-gawk-5.1.0/include:/gnu/store/zyhbjfyqh10yiw1dw1x1i7n70jm9ygdn-make-4.3/include:/gnu/store/cr38d3gvf52ckns2b01lwgw86hk3mvcc-binutils-2.37/include:/gnu/store/h88kd46c8br0wc4i6hq19cjby081ina4-gcc-10.3.0/include:/gnu/store/mjdjgiz9k5rrbj440r16z6p5g33nr7d7-glibc-2.33/include:/gnu/store/z9l8ws05zpfhm5fpl5xl40xxvlbiyqy0-snappy-1.1.9/include:/gnu/store/hnkbafpkvkm1293dbvg7hwyx3yi7jgxd-bitshuffle-for-snappy-0.3.5/include:/gnu/store/k8xlwnnmhgmvzyxxfjq3z3fci73zx7x9-linux-libre-headers-5.10.35/include'
environment variable `CPLUS_INCLUDE_PATH' set to `/gnu/store/l1xmcy7vkq9bzvcx57zc9lyqyhy4qn7b-icedtea-3.19.0-jdk/include:/gnu/store/64zk0izmaframq6cd0xlsmk0rxn3zc52-bzip2-1.0.8/include:/gnu/store/z6bw81zw5b5jm3p02y906p0wnjbjqa7n-xz-5.2.5/include:/gnu/store/jfmrxybjkd0nvh1n34hbzv0lwsnmxz1v-file-5.39/include:/gnu/store/bgyr8c7bl1sqhpapm2kghiya0k6zvi51-gawk-5.1.0/include:/gnu/store/zyhbjfyqh10yiw1dw1x1i7n70jm9ygdn-make-4.3/include:/gnu/store/cr38d3gvf52ckns2b01lwgw86hk3mvcc-binutils-2.37/include:/gnu/store/h88kd46c8br0wc4i6hq19cjby081ina4-gcc-10.3.0/include/c++:/gnu/store/h88kd46c8br0wc4i6hq19cjby081ina4-gcc-10.3.0/include:/gnu/store/mjdjgiz9k5rrbj440r16z6p5g33nr7d7-glibc-2.33/include:/gnu/store/z9l8ws05zpfhm5fpl5xl40xxvlbiyqy0-snappy-1.1.9/include:/gnu/store/hnkbafpkvkm1293dbvg7hwyx3yi7jgxd-bitshuffle-for-snappy-0.3.5/include:/gnu/store/k8xlwnnmhgmvzyxxfjq3z3fci73zx7x9-linux-libre-headers-5.10.35/include'
environment variable `LIBRARY_PATH' set to `/gnu/store/l1xmcy7vkq9bzvcx57zc9lyqyhy4qn7b-icedtea-3.19.0-jdk/lib:/gnu/store/dw5xn0v0ngz49gwlnrxrai9qdd80h021-ant-1.9.15/lib:/gnu/store/d06vlspmlg9qiykcqv167p16apn8z0cf-java-junit-4.12/lib:/gnu/store/djya4k9ywssbgan8s5brhg01r7gaj5yi-java-commons-compress-1.13/lib:/gnu/store/cc2l93zf9amj85i9da3vviq139q06h9b-java-xz-1.9/lib:/gnu/store/64zk0izmaframq6cd0xlsmk0rxn3zc52-bzip2-1.0.8/lib:/gnu/store/z6bw81zw5b5jm3p02y906p0wnjbjqa7n-xz-5.2.5/lib:/gnu/store/jfmrxybjkd0nvh1n34hbzv0lwsnmxz1v-file-5.39/lib:/gnu/store/bgyr8c7bl1sqhpapm2kghiya0k6zvi51-gawk-5.1.0/lib:/gnu/store/cr38d3gvf52ckns2b01lwgw86hk3mvcc-binutils-2.37/lib:/gnu/store/mjdjgiz9k5rrbj440r16z6p5g33nr7d7-glibc-2.33/lib:/gnu/store/88bdm10sayqjnggrxlbdmk3rv1qqdrvl-glibc-2.33-static/lib:/gnu/store/y4x3whxg8i1p9w9vy67lz3cw8xfil8bh-glibc-utf8-locales-2.33/lib:/gnu/store/6bri3m4dfvfa4rp001v7dx23b7h017c9-java-hamcrest-core-1.3/lib:/gnu/store/z9l8ws05zpfhm5fpl5xl40xxvlbiyqy0-snappy-1.1.9/lib:/gnu/store/hnkbafpkvkm1293dbvg7hwyx3yi7jgxd-bitshuffle-for-snappy-0.3.5/lib:/gnu/store/xbff13pfsfskr846x6il8912is3gjq43-apache-commons-parent-pom-41/lib:/gnu/store/pgcbf2m3nzqr8rbi28ykic4lxxpq2bb1-java-hamcrest-parent-pom-1.3/lib:/gnu/store/805dfbw0vrmpsmw8jvlacl4ksyminq2r-apache-parent-pom-18/lib'
environment variable `GUIX_LOCPATH' set to `/gnu/store/y4x3whxg8i1p9w9vy67lz3cw8xfil8bh-glibc-utf8-locales-2.33/lib/locale'
phase `set-paths' succeeded after 0.0 seconds
starting phase `install-locale'
using 'en_US.utf8' locale for category "LC_ALL"
phase `install-locale' succeeded after 0.0 seconds
starting phase `unpack'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/.travis.yml' -> `./.travis.yml'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/build.xml' -> `./build.xml'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/README.md' -> `./README.md'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/.codecov.yml' -> `./.codecov.yml'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/build.gradle' -> `./build.gradle'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/gradlew' -> `./gradlew'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/.gitignore' -> `./.gitignore'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/settings.gradle' -> `./settings.gradle'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/gradle/wrapper/gradle-wrapper.properties' -> `./gradle/wrapper/gradle-wrapper.properties'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/gradle/wrapper/gradle-wrapper.jar' -> `./gradle/wrapper/gradle-wrapper.jar'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/.github/PULL_REQUEST_TEMPLATE.md' -> `./.github/PULL_REQUEST_TEMPLATE.md'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/.github/ISSUE_TEMPLATE.md' -> `./.github/ISSUE_TEMPLATE.md'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/BinaryCigarCodec.java' -> `./src/main/java/htsjdk/samtools/BinaryCigarCodec.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/AlignmentBlock.java' -> `./src/main/java/htsjdk/samtools/AlignmentBlock.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SAMFileWriterFactory.java' -> `./src/main/java/htsjdk/samtools/SAMFileWriterFactory.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/CRAMCRAIIndexer.java' -> `./src/main/java/htsjdk/samtools/CRAMCRAIIndexer.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SAMRecordQueryNameComparator.java' -> `./src/main/java/htsjdk/samtools/SAMRecordQueryNameComparator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SamStreams.java' -> `./src/main/java/htsjdk/samtools/SamStreams.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SAMFileSource.java' -> `./src/main/java/htsjdk/samtools/SAMFileSource.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SAMTextWriter.java' -> `./src/main/java/htsjdk/samtools/SAMTextWriter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SAMLineParser.java' -> `./src/main/java/htsjdk/samtools/SAMLineParser.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SAMTextHeaderCodec.java' -> `./src/main/java/htsjdk/samtools/SAMTextHeaderCodec.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/BinningIndexBuilder.java' -> `./src/main/java/htsjdk/samtools/BinningIndexBuilder.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SAMHeaderRecordComparator.java' -> `./src/main/java/htsjdk/samtools/SAMHeaderRecordComparator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SAMFileHeader.java' -> `./src/main/java/htsjdk/samtools/SAMFileHeader.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/FixBAMFile.java' -> `./src/main/java/htsjdk/samtools/FixBAMFile.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/BAMIndexContent.java' -> `./src/main/java/htsjdk/samtools/BAMIndexContent.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SAMSequenceDictionary.java' -> `./src/main/java/htsjdk/samtools/SAMSequenceDictionary.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/BAMFileConstants.java' -> `./src/main/java/htsjdk/samtools/BAMFileConstants.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SRAFileReader.java' -> `./src/main/java/htsjdk/samtools/SRAFileReader.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/AsyncSAMFileWriter.java' -> `./src/main/java/htsjdk/samtools/AsyncSAMFileWriter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/BinaryBAMIndexWriter.java' -> `./src/main/java/htsjdk/samtools/BinaryBAMIndexWriter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/BAMIndex.java' -> `./src/main/java/htsjdk/samtools/BAMIndex.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/CigarElement.java' -> `./src/main/java/htsjdk/samtools/CigarElement.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SAMSequenceDictionaryCodec.java' -> `./src/main/java/htsjdk/samtools/SAMSequenceDictionaryCodec.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SAMFormatException.java' -> `./src/main/java/htsjdk/samtools/SAMFormatException.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SAMBinaryTagAndUnsignedArrayValue.java' -> `./src/main/java/htsjdk/samtools/SAMBinaryTagAndUnsignedArrayValue.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SAMFileWriterImpl.java' -> `./src/main/java/htsjdk/samtools/SAMFileWriterImpl.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/CRAMContainerStreamWriter.java' -> `./src/main/java/htsjdk/samtools/CRAMContainerStreamWriter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SRAIterator.java' -> `./src/main/java/htsjdk/samtools/SRAIterator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/FileTruncatedException.java' -> `./src/main/java/htsjdk/samtools/FileTruncatedException.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/BAMIndexMetaData.java' -> `./src/main/java/htsjdk/samtools/BAMIndexMetaData.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/GenomicIndexUtil.java' -> `./src/main/java/htsjdk/samtools/GenomicIndexUtil.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SamFlagField.java' -> `./src/main/java/htsjdk/samtools/SamFlagField.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/Chunk.java' -> `./src/main/java/htsjdk/samtools/Chunk.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/ChainedDownsamplingIterator.java' -> `./src/main/java/htsjdk/samtools/ChainedDownsamplingIterator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/Defaults.java' -> `./src/main/java/htsjdk/samtools/Defaults.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/BAMIndexer.java' -> `./src/main/java/htsjdk/samtools/BAMIndexer.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SAMRecordQueryHashComparator.java' -> `./src/main/java/htsjdk/samtools/SAMRecordQueryHashComparator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/CustomReaderFactory.java' -> `./src/main/java/htsjdk/samtools/CustomReaderFactory.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SAMFlag.java' -> `./src/main/java/htsjdk/samtools/SAMFlag.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/BAMFileSpan.java' -> `./src/main/java/htsjdk/samtools/BAMFileSpan.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/BinningIndexContent.java' -> `./src/main/java/htsjdk/samtools/BinningIndexContent.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/HighAccuracyDownsamplingIterator.java' -> `./src/main/java/htsjdk/samtools/HighAccuracyDownsamplingIterator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/TextCigarCodec.java' -> `./src/main/java/htsjdk/samtools/TextCigarCodec.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SamReaderFactory.java' -> `./src/main/java/htsjdk/samtools/SamReaderFactory.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/BAMIteratorFilter.java' -> `./src/main/java/htsjdk/samtools/BAMIteratorFilter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SAMRecordCoordinateComparator.java' -> `./src/main/java/htsjdk/samtools/SAMRecordCoordinateComparator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/BAMQueryMultipleIntervalsIteratorFilter.java' -> `./src/main/java/htsjdk/samtools/BAMQueryMultipleIntervalsIteratorFilter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SRAIndex.java' -> `./src/main/java/htsjdk/samtools/SRAIndex.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/CRAMBAIIndexer.java' -> `./src/main/java/htsjdk/samtools/CRAMBAIIndexer.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/BAMFileWriter.java' -> `./src/main/java/htsjdk/samtools/BAMFileWriter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/ConstantMemoryDownsamplingIterator.java' -> `./src/main/java/htsjdk/samtools/ConstantMemoryDownsamplingIterator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/DuplicateSet.java' -> `./src/main/java/htsjdk/samtools/DuplicateSet.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SAMFileSpan.java' -> `./src/main/java/htsjdk/samtools/SAMFileSpan.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/ComparableSamRecordIterator.java' -> `./src/main/java/htsjdk/samtools/ComparableSamRecordIterator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SAMTools.java' -> `./src/main/java/htsjdk/samtools/SAMTools.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/BAMFileReader.java' -> `./src/main/java/htsjdk/samtools/BAMFileReader.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/DownsamplingIterator.java' -> `./src/main/java/htsjdk/samtools/DownsamplingIterator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/CRAMFileReader.java' -> `./src/main/java/htsjdk/samtools/CRAMFileReader.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SAMValidationError.java' -> `./src/main/java/htsjdk/samtools/SAMValidationError.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/BrowseableBAMIndex.java' -> `./src/main/java/htsjdk/samtools/BrowseableBAMIndex.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/TextTagCodec.java' -> `./src/main/java/htsjdk/samtools/TextTagCodec.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SAMRecordUtil.java' -> `./src/main/java/htsjdk/samtools/SAMRecordUtil.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/BAMRecord.java' -> `./src/main/java/htsjdk/samtools/BAMRecord.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SAMTestUtil.java' -> `./src/main/java/htsjdk/samtools/SAMTestUtil.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SAMException.java' -> `./src/main/java/htsjdk/samtools/SAMException.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SamReader.java' -> `./src/main/java/htsjdk/samtools/SamReader.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/ReservedTagConstants.java' -> `./src/main/java/htsjdk/samtools/ReservedTagConstants.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/QueryInterval.java' -> `./src/main/java/htsjdk/samtools/QueryInterval.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SAMRecordSetBuilder.java' -> `./src/main/java/htsjdk/samtools/SAMRecordSetBuilder.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/CRAMFileWriter.java' -> `./src/main/java/htsjdk/samtools/CRAMFileWriter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/BinList.java' -> `./src/main/java/htsjdk/samtools/BinList.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/BAMRecordCodec.java' -> `./src/main/java/htsjdk/samtools/BAMRecordCodec.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SAMUtils.java' -> `./src/main/java/htsjdk/samtools/SAMUtils.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/BAMIndexWriter.java' -> `./src/main/java/htsjdk/samtools/BAMIndexWriter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/ValidationStringency.java' -> `./src/main/java/htsjdk/samtools/ValidationStringency.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SAMTag.java' -> `./src/main/java/htsjdk/samtools/SAMTag.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/DiskBasedBAMFileIndex.java' -> `./src/main/java/htsjdk/samtools/DiskBasedBAMFileIndex.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/TextualBAMIndexWriter.java' -> `./src/main/java/htsjdk/samtools/TextualBAMIndexWriter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/CachingBAMFileIndex.java' -> `./src/main/java/htsjdk/samtools/CachingBAMFileIndex.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/CigarOperator.java' -> `./src/main/java/htsjdk/samtools/CigarOperator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SamPairUtil.java' -> `./src/main/java/htsjdk/samtools/SamPairUtil.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SAMRecordDuplicateComparator.java' -> `./src/main/java/htsjdk/samtools/SAMRecordDuplicateComparator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SAMReadGroupRecord.java' -> `./src/main/java/htsjdk/samtools/SAMReadGroupRecord.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/Cigar.java' -> `./src/main/java/htsjdk/samtools/Cigar.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SamFileHeaderMerger.java' -> `./src/main/java/htsjdk/samtools/SamFileHeaderMerger.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/LinearIndex.java' -> `./src/main/java/htsjdk/samtools/LinearIndex.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/BamIndexValidator.java' -> `./src/main/java/htsjdk/samtools/BamIndexValidator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/CRAMIterator.java' -> `./src/main/java/htsjdk/samtools/CRAMIterator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SAMProgramRecord.java' -> `./src/main/java/htsjdk/samtools/SAMProgramRecord.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/CoordinateSortedPairInfoMap.java' -> `./src/main/java/htsjdk/samtools/CoordinateSortedPairInfoMap.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/NotPrimarySkippingIterator.java' -> `./src/main/java/htsjdk/samtools/NotPrimarySkippingIterator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/DownsamplingIteratorFactory.java' -> `./src/main/java/htsjdk/samtools/DownsamplingIteratorFactory.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SamIndexes.java' -> `./src/main/java/htsjdk/samtools/SamIndexes.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/BamFileIoUtils.java' -> `./src/main/java/htsjdk/samtools/BamFileIoUtils.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SamInputResource.java' -> `./src/main/java/htsjdk/samtools/SamInputResource.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SAMRecord.java' -> `./src/main/java/htsjdk/samtools/SAMRecord.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SAMRecordIterator.java' -> `./src/main/java/htsjdk/samtools/SAMRecordIterator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/DuplicateScoringStrategy.java' -> `./src/main/java/htsjdk/samtools/DuplicateScoringStrategy.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/Bin.java' -> `./src/main/java/htsjdk/samtools/Bin.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/AbstractSAMHeaderRecord.java' -> `./src/main/java/htsjdk/samtools/AbstractSAMHeaderRecord.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/StreamInflatingIndexingOutputStream.java' -> `./src/main/java/htsjdk/samtools/StreamInflatingIndexingOutputStream.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SQTagUtil.java' -> `./src/main/java/htsjdk/samtools/SQTagUtil.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/BinaryTagCodec.java' -> `./src/main/java/htsjdk/samtools/BinaryTagCodec.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SamFiles.java' -> `./src/main/java/htsjdk/samtools/SamFiles.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/MergingSamRecordIterator.java' -> `./src/main/java/htsjdk/samtools/MergingSamRecordIterator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SAMRecordComparator.java' -> `./src/main/java/htsjdk/samtools/SAMRecordComparator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SAMRecordFactory.java' -> `./src/main/java/htsjdk/samtools/SAMRecordFactory.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SamFileValidator.java' -> `./src/main/java/htsjdk/samtools/SamFileValidator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SAMSequenceRecord.java' -> `./src/main/java/htsjdk/samtools/SAMSequenceRecord.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/DefaultSAMRecordFactory.java' -> `./src/main/java/htsjdk/samtools/DefaultSAMRecordFactory.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SecondaryOrSupplementarySkippingIterator.java' -> `./src/main/java/htsjdk/samtools/SecondaryOrSupplementarySkippingIterator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/AbstractBAMFileIndex.java' -> `./src/main/java/htsjdk/samtools/AbstractBAMFileIndex.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/TagValueAndUnsignedArrayFlag.java' -> `./src/main/java/htsjdk/samtools/TagValueAndUnsignedArrayFlag.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SAMBinaryTagAndValue.java' -> `./src/main/java/htsjdk/samtools/SAMBinaryTagAndValue.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SAMSortOrderChecker.java' -> `./src/main/java/htsjdk/samtools/SAMSortOrderChecker.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SAMFileWriter.java' -> `./src/main/java/htsjdk/samtools/SAMFileWriter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/DuplicateSetIterator.java' -> `./src/main/java/htsjdk/samtools/DuplicateSetIterator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SAMTagUtil.java' -> `./src/main/java/htsjdk/samtools/SAMTagUtil.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/SAMTextReader.java' -> `./src/main/java/htsjdk/samtools/SAMTextReader.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/sra/SRAUnalignmentIterator.java' -> `./src/main/java/htsjdk/samtools/sra/SRAUnalignmentIterator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/sra/ReferenceCache.java' -> `./src/main/java/htsjdk/samtools/sra/ReferenceCache.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/sra/SRALazyRecord.java' -> `./src/main/java/htsjdk/samtools/sra/SRALazyRecord.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/sra/SRAIndexedSequenceFile.java' -> `./src/main/java/htsjdk/samtools/sra/SRAIndexedSequenceFile.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/sra/SRAUtils.java' -> `./src/main/java/htsjdk/samtools/sra/SRAUtils.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/sra/SRAAlignmentIterator.java' -> `./src/main/java/htsjdk/samtools/sra/SRAAlignmentIterator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/sra/SRAAccession.java' -> `./src/main/java/htsjdk/samtools/sra/SRAAccession.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/IterableAdapter.java' -> `./src/main/java/htsjdk/samtools/util/IterableAdapter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/IntervalTreeMap.java' -> `./src/main/java/htsjdk/samtools/util/IntervalTreeMap.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/Tuple.java' -> `./src/main/java/htsjdk/samtools/util/Tuple.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/ListMap.java' -> `./src/main/java/htsjdk/samtools/util/ListMap.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/StopWatch.java' -> `./src/main/java/htsjdk/samtools/util/StopWatch.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/FileAppendStreamLRUCache.java' -> `./src/main/java/htsjdk/samtools/util/FileAppendStreamLRUCache.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/AbstractProgressLogger.java' -> `./src/main/java/htsjdk/samtools/util/AbstractProgressLogger.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/IterableOnceIterator.java' -> `./src/main/java/htsjdk/samtools/util/IterableOnceIterator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/RelativeIso8601Date.java' -> `./src/main/java/htsjdk/samtools/util/RelativeIso8601Date.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/PositionalOutputStream.java' -> `./src/main/java/htsjdk/samtools/util/PositionalOutputStream.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/EdgingRecordAndOffset.java' -> `./src/main/java/htsjdk/samtools/util/EdgingRecordAndOffset.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/BlockCompressedStreamConstants.java' -> `./src/main/java/htsjdk/samtools/util/BlockCompressedStreamConstants.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/AbstractIterator.java' -> `./src/main/java/htsjdk/samtools/util/AbstractIterator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/Histogram.java' -> `./src/main/java/htsjdk/samtools/util/Histogram.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/BinaryCodec.java' -> `./src/main/java/htsjdk/samtools/util/BinaryCodec.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/MergingIterator.java' -> `./src/main/java/htsjdk/samtools/util/MergingIterator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/BlockCompressedInputStream.java' -> `./src/main/java/htsjdk/samtools/util/BlockCompressedInputStream.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/SnappyLoader.java' -> `./src/main/java/htsjdk/samtools/util/SnappyLoader.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/IntervalUtil.java' -> `./src/main/java/htsjdk/samtools/util/IntervalUtil.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/Locatable.java' -> `./src/main/java/htsjdk/samtools/util/Locatable.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/Md5CalculatingInputStream.java' -> `./src/main/java/htsjdk/samtools/util/Md5CalculatingInputStream.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/IntervalListReferenceSequenceMask.java' -> `./src/main/java/htsjdk/samtools/util/IntervalListReferenceSequenceMask.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/Lazy.java' -> `./src/main/java/htsjdk/samtools/util/Lazy.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/ProgressLogger.java' -> `./src/main/java/htsjdk/samtools/util/ProgressLogger.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/AbstractAsyncWriter.java' -> `./src/main/java/htsjdk/samtools/util/AbstractAsyncWriter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/RuntimeEOFException.java' -> `./src/main/java/htsjdk/samtools/util/RuntimeEOFException.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/DelegatingIterator.java' -> `./src/main/java/htsjdk/samtools/util/DelegatingIterator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/AbstractLocusIterator.java' -> `./src/main/java/htsjdk/samtools/util/AbstractLocusIterator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/CustomGzipOutputStream.java' -> `./src/main/java/htsjdk/samtools/util/CustomGzipOutputStream.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/FastLineReader.java' -> `./src/main/java/htsjdk/samtools/util/FastLineReader.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/FastqQualityFormat.java' -> `./src/main/java/htsjdk/samtools/util/FastqQualityFormat.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/PeekIterator.java' -> `./src/main/java/htsjdk/samtools/util/PeekIterator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/SamLocusIterator.java' -> `./src/main/java/htsjdk/samtools/util/SamLocusIterator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/OverlapDetector.java' -> `./src/main/java/htsjdk/samtools/util/OverlapDetector.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/CollectionUtil.java' -> `./src/main/java/htsjdk/samtools/util/CollectionUtil.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/StringLineReader.java' -> `./src/main/java/htsjdk/samtools/util/StringLineReader.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/IntervalTree.java' -> `./src/main/java/htsjdk/samtools/util/IntervalTree.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/ReferenceSequenceMask.java' -> `./src/main/java/htsjdk/samtools/util/ReferenceSequenceMask.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/WholeGenomeReferenceSequenceMask.java' -> `./src/main/java/htsjdk/samtools/util/WholeGenomeReferenceSequenceMask.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/TempStreamFactory.java' -> `./src/main/java/htsjdk/samtools/util/TempStreamFactory.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/SortingLongCollection.java' -> `./src/main/java/htsjdk/samtools/util/SortingLongCollection.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/CoordSpanInputSteam.java' -> `./src/main/java/htsjdk/samtools/util/CoordSpanInputSteam.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/LocusImpl.java' -> `./src/main/java/htsjdk/samtools/util/LocusImpl.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/AsyncBufferedIterator.java' -> `./src/main/java/htsjdk/samtools/util/AsyncBufferedIterator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/SamRecordIntervalIteratorFactory.java' -> `./src/main/java/htsjdk/samtools/util/SamRecordIntervalIteratorFactory.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/ResourceLimitedMap.java' -> `./src/main/java/htsjdk/samtools/util/ResourceLimitedMap.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/Iso8601Date.java' -> `./src/main/java/htsjdk/samtools/util/Iso8601Date.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/DiskBackedQueue.java' -> `./src/main/java/htsjdk/samtools/util/DiskBackedQueue.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/Interval.java' -> `./src/main/java/htsjdk/samtools/util/Interval.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/LocusComparator.java' -> `./src/main/java/htsjdk/samtools/util/LocusComparator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/EdgeReadIterator.java' -> `./src/main/java/htsjdk/samtools/util/EdgeReadIterator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/BufferedLineReader.java' -> `./src/main/java/htsjdk/samtools/util/BufferedLineReader.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/AsciiWriter.java' -> `./src/main/java/htsjdk/samtools/util/AsciiWriter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/AbstractLocusInfo.java' -> `./src/main/java/htsjdk/samtools/util/AbstractLocusInfo.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/RuntimeScriptException.java' -> `./src/main/java/htsjdk/samtools/util/RuntimeScriptException.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/BlockCompressedFilePointerUtil.java' -> `./src/main/java/htsjdk/samtools/util/BlockCompressedFilePointerUtil.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/Murmur3.java' -> `./src/main/java/htsjdk/samtools/util/Murmur3.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/CloseableIterator.java' -> `./src/main/java/htsjdk/samtools/util/CloseableIterator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/AsyncBlockCompressedInputStream.java' -> `./src/main/java/htsjdk/samtools/util/AsyncBlockCompressedInputStream.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/FormatUtil.java' -> `./src/main/java/htsjdk/samtools/util/FormatUtil.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/CoordMath.java' -> `./src/main/java/htsjdk/samtools/util/CoordMath.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/Iterables.java' -> `./src/main/java/htsjdk/samtools/util/Iterables.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/LineReader.java' -> `./src/main/java/htsjdk/samtools/util/LineReader.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/RuntimeIOException.java' -> `./src/main/java/htsjdk/samtools/util/RuntimeIOException.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/StringUtil.java' -> `./src/main/java/htsjdk/samtools/util/StringUtil.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/CodeUtil.java' -> `./src/main/java/htsjdk/samtools/util/CodeUtil.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/HttpUtils.java' -> `./src/main/java/htsjdk/samtools/util/HttpUtils.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/ProcessExecutor.java' -> `./src/main/java/htsjdk/samtools/util/ProcessExecutor.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/LocationAware.java' -> `./src/main/java/htsjdk/samtools/util/LocationAware.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/SamRecordWithOrdinal.java' -> `./src/main/java/htsjdk/samtools/util/SamRecordWithOrdinal.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/SolexaQualityConverter.java' -> `./src/main/java/htsjdk/samtools/util/SolexaQualityConverter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/ResourceLimitedMapFunctor.java' -> `./src/main/java/htsjdk/samtools/util/ResourceLimitedMapFunctor.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/SequenceUtil.java' -> `./src/main/java/htsjdk/samtools/util/SequenceUtil.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/DateParser.java' -> `./src/main/java/htsjdk/samtools/util/DateParser.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/QualityEncodingDetector.java' -> `./src/main/java/htsjdk/samtools/util/QualityEncodingDetector.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/SortingCollection.java' -> `./src/main/java/htsjdk/samtools/util/SortingCollection.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/AbstractRecordAndOffset.java' -> `./src/main/java/htsjdk/samtools/util/AbstractRecordAndOffset.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/IOUtil.java' -> `./src/main/java/htsjdk/samtools/util/IOUtil.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/QualityUtil.java' -> `./src/main/java/htsjdk/samtools/util/QualityUtil.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java' -> `./src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/SamRecordTrackingBuffer.java' -> `./src/main/java/htsjdk/samtools/util/SamRecordTrackingBuffer.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/TestUtil.java' -> `./src/main/java/htsjdk/samtools/util/TestUtil.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/ProgressLoggerInterface.java' -> `./src/main/java/htsjdk/samtools/util/ProgressLoggerInterface.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/CloserUtil.java' -> `./src/main/java/htsjdk/samtools/util/CloserUtil.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/BlockGunzipper.java' -> `./src/main/java/htsjdk/samtools/util/BlockGunzipper.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/Locus.java' -> `./src/main/java/htsjdk/samtools/util/Locus.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/ComparableTuple.java' -> `./src/main/java/htsjdk/samtools/util/ComparableTuple.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/Log.java' -> `./src/main/java/htsjdk/samtools/util/Log.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/TrimmingUtil.java' -> `./src/main/java/htsjdk/samtools/util/TrimmingUtil.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/IntervalList.java' -> `./src/main/java/htsjdk/samtools/util/IntervalList.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/Md5CalculatingOutputStream.java' -> `./src/main/java/htsjdk/samtools/util/Md5CalculatingOutputStream.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/PeekableIterator.java' -> `./src/main/java/htsjdk/samtools/util/PeekableIterator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/CigarUtil.java' -> `./src/main/java/htsjdk/samtools/util/CigarUtil.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/ftp/FTPReply.java' -> `./src/main/java/htsjdk/samtools/util/ftp/FTPReply.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/ftp/FTPUtils.java' -> `./src/main/java/htsjdk/samtools/util/ftp/FTPUtils.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/ftp/FTPStream.java' -> `./src/main/java/htsjdk/samtools/util/ftp/FTPStream.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/ftp/FTPClient.java' -> `./src/main/java/htsjdk/samtools/util/ftp/FTPClient.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/zip/DeflaterFactory.java' -> `./src/main/java/htsjdk/samtools/util/zip/DeflaterFactory.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/util/zip/InflaterFactory.java' -> `./src/main/java/htsjdk/samtools/util/zip/InflaterFactory.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/apps/TimeChannel.java' -> `./src/main/java/htsjdk/samtools/apps/TimeChannel.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/apps/TimeRandomAccessFile.java' -> `./src/main/java/htsjdk/samtools/apps/TimeRandomAccessFile.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/filter/DuplicateReadFilter.java' -> `./src/main/java/htsjdk/samtools/filter/DuplicateReadFilter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/filter/FailsVendorReadQualityFilter.java' -> `./src/main/java/htsjdk/samtools/filter/FailsVendorReadQualityFilter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/filter/AlignedFilter.java' -> `./src/main/java/htsjdk/samtools/filter/AlignedFilter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/filter/ReadNameFilter.java' -> `./src/main/java/htsjdk/samtools/filter/ReadNameFilter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/filter/IntervalFilter.java' -> `./src/main/java/htsjdk/samtools/filter/IntervalFilter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/filter/NotPrimaryAlignmentFilter.java' -> `./src/main/java/htsjdk/samtools/filter/NotPrimaryAlignmentFilter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/filter/SamRecordFilter.java' -> `./src/main/java/htsjdk/samtools/filter/SamRecordFilter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/filter/AggregateFilter.java' -> `./src/main/java/htsjdk/samtools/filter/AggregateFilter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/filter/TagFilter.java' -> `./src/main/java/htsjdk/samtools/filter/TagFilter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/filter/SecondaryAlignmentFilter.java' -> `./src/main/java/htsjdk/samtools/filter/SecondaryAlignmentFilter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/filter/InsertSizeFilter.java' -> `./src/main/java/htsjdk/samtools/filter/InsertSizeFilter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/filter/AbstractJavascriptFilter.java' -> `./src/main/java/htsjdk/samtools/filter/AbstractJavascriptFilter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/filter/OverclippedReadFilter.java' -> `./src/main/java/htsjdk/samtools/filter/OverclippedReadFilter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/filter/WholeReadClippedFilter.java' -> `./src/main/java/htsjdk/samtools/filter/WholeReadClippedFilter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/filter/SecondaryOrSupplementaryFilter.java' -> `./src/main/java/htsjdk/samtools/filter/SecondaryOrSupplementaryFilter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/filter/SolexaNoiseFilter.java' -> `./src/main/java/htsjdk/samtools/filter/SolexaNoiseFilter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/filter/FilteringIterator.java' -> `./src/main/java/htsjdk/samtools/filter/FilteringIterator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/filter/IntervalKeepPairFilter.java' -> `./src/main/java/htsjdk/samtools/filter/IntervalKeepPairFilter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/filter/MappingQualityFilter.java' -> `./src/main/java/htsjdk/samtools/filter/MappingQualityFilter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/filter/FilteringSamIterator.java' -> `./src/main/java/htsjdk/samtools/filter/FilteringSamIterator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/filter/JavascriptSamRecordFilter.java' -> `./src/main/java/htsjdk/samtools/filter/JavascriptSamRecordFilter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/reference/FastaSequenceIndex.java' -> `./src/main/java/htsjdk/samtools/reference/FastaSequenceIndex.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/reference/AbstractFastaSequenceFile.java' -> `./src/main/java/htsjdk/samtools/reference/AbstractFastaSequenceFile.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/reference/FastaSequenceIndexCreator.java' -> `./src/main/java/htsjdk/samtools/reference/FastaSequenceIndexCreator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/reference/ReferenceSequenceFile.java' -> `./src/main/java/htsjdk/samtools/reference/ReferenceSequenceFile.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/reference/ReferenceSequence.java' -> `./src/main/java/htsjdk/samtools/reference/ReferenceSequence.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/reference/FastaSequenceFile.java' -> `./src/main/java/htsjdk/samtools/reference/FastaSequenceFile.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/reference/ReferenceSequenceFileWalker.java' -> `./src/main/java/htsjdk/samtools/reference/ReferenceSequenceFileWalker.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/reference/ReferenceSequenceFileFactory.java' -> `./src/main/java/htsjdk/samtools/reference/ReferenceSequenceFileFactory.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/reference/IndexedFastaSequenceFile.java' -> `./src/main/java/htsjdk/samtools/reference/IndexedFastaSequenceFile.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/example/ExampleSamUsage.java' -> `./src/main/java/htsjdk/samtools/example/ExampleSamUsage.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/example/PrintReadsExample.java' -> `./src/main/java/htsjdk/samtools/example/PrintReadsExample.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/liftover/Chain.java' -> `./src/main/java/htsjdk/samtools/liftover/Chain.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/liftover/LiftOver.java' -> `./src/main/java/htsjdk/samtools/liftover/LiftOver.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/metrics/MetricsFile.java' -> `./src/main/java/htsjdk/samtools/metrics/MetricsFile.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/metrics/Header.java' -> `./src/main/java/htsjdk/samtools/metrics/Header.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/metrics/VersionHeader.java' -> `./src/main/java/htsjdk/samtools/metrics/VersionHeader.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/metrics/StringHeader.java' -> `./src/main/java/htsjdk/samtools/metrics/StringHeader.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/metrics/MetricBase.java' -> `./src/main/java/htsjdk/samtools/metrics/MetricBase.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/CRAMException.java' -> `./src/main/java/htsjdk/samtools/cram/CRAMException.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/CRAIEntry.java' -> `./src/main/java/htsjdk/samtools/cram/CRAIEntry.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/CRAIIndex.java' -> `./src/main/java/htsjdk/samtools/cram/CRAIIndex.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/structure/ReadTag.java' -> `./src/main/java/htsjdk/samtools/cram/structure/ReadTag.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/structure/ContainerIO.java' -> `./src/main/java/htsjdk/samtools/cram/structure/ContainerIO.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/structure/BlockCompressionMethod.java' -> `./src/main/java/htsjdk/samtools/cram/structure/BlockCompressionMethod.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/structure/EncodingKey.java' -> `./src/main/java/htsjdk/samtools/cram/structure/EncodingKey.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/structure/Container.java' -> `./src/main/java/htsjdk/samtools/cram/structure/Container.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/structure/EncodingID.java' -> `./src/main/java/htsjdk/samtools/cram/structure/EncodingID.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/structure/SubstitutionMatrix.java' -> `./src/main/java/htsjdk/samtools/cram/structure/SubstitutionMatrix.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/structure/ContainerHeaderIO.java' -> `./src/main/java/htsjdk/samtools/cram/structure/ContainerHeaderIO.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/structure/EncodingParams.java' -> `./src/main/java/htsjdk/samtools/cram/structure/EncodingParams.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/structure/AlignmentSpan.java' -> `./src/main/java/htsjdk/samtools/cram/structure/AlignmentSpan.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/structure/CramHeader.java' -> `./src/main/java/htsjdk/samtools/cram/structure/CramHeader.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/structure/SliceIO.java' -> `./src/main/java/htsjdk/samtools/cram/structure/SliceIO.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/structure/Slice.java' -> `./src/main/java/htsjdk/samtools/cram/structure/Slice.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/structure/CramCompressionRecord.java' -> `./src/main/java/htsjdk/samtools/cram/structure/CramCompressionRecord.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/structure/Block.java' -> `./src/main/java/htsjdk/samtools/cram/structure/Block.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/structure/CompressionHeader.java' -> `./src/main/java/htsjdk/samtools/cram/structure/CompressionHeader.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/structure/BlockContentType.java' -> `./src/main/java/htsjdk/samtools/cram/structure/BlockContentType.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/io/CramInt.java' -> `./src/main/java/htsjdk/samtools/cram/io/CramInt.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/io/LTF8.java' -> `./src/main/java/htsjdk/samtools/cram/io/LTF8.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/io/InputStreamUtils.java' -> `./src/main/java/htsjdk/samtools/cram/io/InputStreamUtils.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/io/BitOutputStream.java' -> `./src/main/java/htsjdk/samtools/cram/io/BitOutputStream.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/io/ExposedByteArrayOutputStream.java' -> `./src/main/java/htsjdk/samtools/cram/io/ExposedByteArrayOutputStream.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/io/DefaultBitInputStream.java' -> `./src/main/java/htsjdk/samtools/cram/io/DefaultBitInputStream.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/io/ITF8.java' -> `./src/main/java/htsjdk/samtools/cram/io/ITF8.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/io/ExternalCompression.java' -> `./src/main/java/htsjdk/samtools/cram/io/ExternalCompression.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/io/CramArray.java' -> `./src/main/java/htsjdk/samtools/cram/io/CramArray.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/io/DefaultBitOutputStream.java' -> `./src/main/java/htsjdk/samtools/cram/io/DefaultBitOutputStream.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/io/CRC32OutputStream.java' -> `./src/main/java/htsjdk/samtools/cram/io/CRC32OutputStream.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/io/CountingInputStream.java' -> `./src/main/java/htsjdk/samtools/cram/io/CountingInputStream.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/io/CRC32InputStream.java' -> `./src/main/java/htsjdk/samtools/cram/io/CRC32InputStream.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/io/BitInputStream.java' -> `./src/main/java/htsjdk/samtools/cram/io/BitInputStream.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/build/CramSpanContainerIterator.java' -> `./src/main/java/htsjdk/samtools/cram/build/CramSpanContainerIterator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/build/ContainerParser.java' -> `./src/main/java/htsjdk/samtools/cram/build/ContainerParser.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/build/Sam2CramRecordFactory.java' -> `./src/main/java/htsjdk/samtools/cram/build/Sam2CramRecordFactory.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/build/CramNormalizer.java' -> `./src/main/java/htsjdk/samtools/cram/build/CramNormalizer.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/build/CompressionHeaderFactory.java' -> `./src/main/java/htsjdk/samtools/cram/build/CompressionHeaderFactory.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/build/Cram2SamRecordFactory.java' -> `./src/main/java/htsjdk/samtools/cram/build/Cram2SamRecordFactory.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/build/ContainerFactory.java' -> `./src/main/java/htsjdk/samtools/cram/build/ContainerFactory.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/build/Utils.java' -> `./src/main/java/htsjdk/samtools/cram/build/Utils.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/build/CramIO.java' -> `./src/main/java/htsjdk/samtools/cram/build/CramIO.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/build/CramContainerIterator.java' -> `./src/main/java/htsjdk/samtools/cram/build/CramContainerIterator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/lossy/ReadCategoryType.java' -> `./src/main/java/htsjdk/samtools/cram/lossy/ReadCategoryType.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/lossy/QualityScoreTreatmentType.java' -> `./src/main/java/htsjdk/samtools/cram/lossy/QualityScoreTreatmentType.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/lossy/PreservationPolicy.java' -> `./src/main/java/htsjdk/samtools/cram/lossy/PreservationPolicy.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/lossy/BaseCategoryType.java' -> `./src/main/java/htsjdk/samtools/cram/lossy/BaseCategoryType.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/lossy/ReadCategory.java' -> `./src/main/java/htsjdk/samtools/cram/lossy/ReadCategory.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/lossy/QualityScoreTreatment.java' -> `./src/main/java/htsjdk/samtools/cram/lossy/QualityScoreTreatment.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/lossy/QualityScorePreservation.java' -> `./src/main/java/htsjdk/samtools/cram/lossy/QualityScorePreservation.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/lossy/BaseCategory.java' -> `./src/main/java/htsjdk/samtools/cram/lossy/BaseCategory.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/lossy/Binning.java' -> `./src/main/java/htsjdk/samtools/cram/lossy/Binning.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/ref/ReferenceRegion.java' -> `./src/main/java/htsjdk/samtools/cram/ref/ReferenceRegion.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/ref/ReferenceSource.java' -> `./src/main/java/htsjdk/samtools/cram/ref/ReferenceSource.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/ref/EnaRefService.java' -> `./src/main/java/htsjdk/samtools/cram/ref/EnaRefService.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/ref/InMemoryReferenceSequenceFile.java' -> `./src/main/java/htsjdk/samtools/cram/ref/InMemoryReferenceSequenceFile.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/ref/CRAMReferenceSource.java' -> `./src/main/java/htsjdk/samtools/cram/ref/CRAMReferenceSource.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/ref/ReferenceTracks.java' -> `./src/main/java/htsjdk/samtools/cram/ref/ReferenceTracks.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/common/CramVersions.java' -> `./src/main/java/htsjdk/samtools/cram/common/CramVersions.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/common/IntHashMap.java' -> `./src/main/java/htsjdk/samtools/cram/common/IntHashMap.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/common/MutableInt.java' -> `./src/main/java/htsjdk/samtools/cram/common/MutableInt.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/common/Version.java' -> `./src/main/java/htsjdk/samtools/cram/common/Version.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/common/CramVersionPolicies.java' -> `./src/main/java/htsjdk/samtools/cram/common/CramVersionPolicies.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/digest/IntegerSumCombine.java' -> `./src/main/java/htsjdk/samtools/cram/digest/IntegerSumCombine.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/digest/MessageDigestHasher.java' -> `./src/main/java/htsjdk/samtools/cram/digest/MessageDigestHasher.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/digest/ByteSumCombine.java' -> `./src/main/java/htsjdk/samtools/cram/digest/ByteSumCombine.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/digest/Crc32Hasher.java' -> `./src/main/java/htsjdk/samtools/cram/digest/Crc32Hasher.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/digest/AbstractSerialDigest.java' -> `./src/main/java/htsjdk/samtools/cram/digest/AbstractSerialDigest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/digest/Combine.java' -> `./src/main/java/htsjdk/samtools/cram/digest/Combine.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/digest/ContentDigests.java' -> `./src/main/java/htsjdk/samtools/cram/digest/ContentDigests.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/digest/SERIES.java' -> `./src/main/java/htsjdk/samtools/cram/digest/SERIES.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/BetaIntegerCodec.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/BetaIntegerCodec.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/ExternalByteArrayCodec.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/ExternalByteArrayCodec.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/NullEncoding.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/NullEncoding.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/GolombLongCodec.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/GolombLongCodec.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/EncodingFactory.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/EncodingFactory.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/NullCodec.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/NullCodec.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/ExternalLongCodec.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/ExternalLongCodec.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/DataSeriesType.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/DataSeriesType.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/AbstractBitCodec.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/AbstractBitCodec.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/DataSeries.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/DataSeries.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/ExternalByteArrayEncoding.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/ExternalByteArrayEncoding.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/GolombRiceIntegerEncoding.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/GolombRiceIntegerEncoding.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/ExternalCompressor.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/ExternalCompressor.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/GammaIntegerCodec.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/GammaIntegerCodec.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/GolombIntegerEncoding.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/GolombIntegerEncoding.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/ExternalIntegerEncoding.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/ExternalIntegerEncoding.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/ExternalByteEncoding.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/ExternalByteEncoding.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/GammaIntegerEncoding.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/GammaIntegerEncoding.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/SubexponentialIntegerCodec.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/SubexponentialIntegerCodec.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/ExternalLongEncoding.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/ExternalLongEncoding.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/ExternalByteCodec.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/ExternalByteCodec.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/ExternalIntegerCodec.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/ExternalIntegerCodec.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/BetaIntegerEncoding.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/BetaIntegerEncoding.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/SubexponentialIntegerEncoding.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/SubexponentialIntegerEncoding.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/GolombRiceIntegerCodec.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/GolombRiceIntegerCodec.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/ByteArrayStopEncoding.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/ByteArrayStopEncoding.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/DataSeriesMap.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/DataSeriesMap.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/GolombIntegerCodec.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/GolombIntegerCodec.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/ByteArrayLenEncoding.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/ByteArrayLenEncoding.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/Encoding.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/Encoding.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/BitCodec.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/BitCodec.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/GolombLongEncoding.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/GolombLongEncoding.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/reader/AbstractReader.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/reader/AbstractReader.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/reader/RefSeqIdReader.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/reader/RefSeqIdReader.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/reader/DataReader.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/reader/DataReader.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/reader/CramRecordReader.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/reader/CramRecordReader.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/reader/DataReaderFactory.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/reader/DataReaderFactory.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/readfeatures/Scores.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/readfeatures/Scores.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/readfeatures/InsertBase.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/readfeatures/InsertBase.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/readfeatures/Insertion.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/readfeatures/Insertion.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/readfeatures/HardClip.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/readfeatures/HardClip.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/readfeatures/Bases.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/readfeatures/Bases.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/readfeatures/SoftClip.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/readfeatures/SoftClip.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/readfeatures/BaseQualityScore.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/readfeatures/BaseQualityScore.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/readfeatures/ReadBase.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/readfeatures/ReadBase.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/readfeatures/ReadFeature.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/readfeatures/ReadFeature.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/readfeatures/Padding.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/readfeatures/Padding.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/readfeatures/Deletion.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/readfeatures/Deletion.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/readfeatures/Substitution.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/readfeatures/Substitution.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/readfeatures/RefSkip.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/readfeatures/RefSkip.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/huffman/HuffmanLeaf.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/huffman/HuffmanLeaf.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/huffman/HuffmanTree.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/huffman/HuffmanTree.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/huffman/HuffmanNode.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/huffman/HuffmanNode.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/huffman/HuffmanCode.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/huffman/HuffmanCode.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/huffman/codec/HuffmanIntegerEncoding.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/huffman/codec/HuffmanIntegerEncoding.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/huffman/codec/HuffmanIntHelper.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/huffman/codec/HuffmanIntHelper.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/huffman/codec/CanonicalHuffmanIntegerCodec.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/huffman/codec/CanonicalHuffmanIntegerCodec.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/huffman/codec/HuffmanByteEncoding.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/huffman/codec/HuffmanByteEncoding.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/huffman/codec/HuffmanByteHelper.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/huffman/codec/HuffmanByteHelper.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/huffman/codec/HuffmanParamsCalculator.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/huffman/codec/HuffmanParamsCalculator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/huffman/codec/HuffmanBitCode.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/huffman/codec/HuffmanBitCode.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/huffman/codec/CanonicalHuffmanByteCodec.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/huffman/codec/CanonicalHuffmanByteCodec.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/rans/RANS.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/rans/RANS.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/rans/D14.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/rans/D14.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/rans/E04.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/rans/E04.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/rans/D04.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/rans/D04.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/rans/Utils.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/rans/Utils.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/rans/Decoding.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/rans/Decoding.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/rans/E14.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/rans/E14.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/rans/Constants.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/rans/Constants.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/rans/Frequencies.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/rans/Frequencies.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/rans/Encoding.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/rans/Encoding.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/writer/DataWriterFactory.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/writer/DataWriterFactory.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/writer/DataWriter.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/writer/DataWriter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/cram/encoding/writer/Writer.java' -> `./src/main/java/htsjdk/samtools/cram/encoding/writer/Writer.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/seekablestream/ByteArraySeekableStream.java' -> `./src/main/java/htsjdk/samtools/seekablestream/ByteArraySeekableStream.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/seekablestream/SeekableStreamFactory.java' -> `./src/main/java/htsjdk/samtools/seekablestream/SeekableStreamFactory.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/seekablestream/SeekableBufferedStream.java' -> `./src/main/java/htsjdk/samtools/seekablestream/SeekableBufferedStream.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/seekablestream/SeekableFTPStream.java' -> `./src/main/java/htsjdk/samtools/seekablestream/SeekableFTPStream.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/seekablestream/ISeekableStreamFactory.java' -> `./src/main/java/htsjdk/samtools/seekablestream/ISeekableStreamFactory.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/seekablestream/SeekableMemoryStream.java' -> `./src/main/java/htsjdk/samtools/seekablestream/SeekableMemoryStream.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/seekablestream/SeekableFTPStreamHelper.java' -> `./src/main/java/htsjdk/samtools/seekablestream/SeekableFTPStreamHelper.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/seekablestream/UserPasswordInput.java' -> `./src/main/java/htsjdk/samtools/seekablestream/UserPasswordInput.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/seekablestream/SeekableFileStream.java' -> `./src/main/java/htsjdk/samtools/seekablestream/SeekableFileStream.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/seekablestream/SeekableHTTPStream.java' -> `./src/main/java/htsjdk/samtools/seekablestream/SeekableHTTPStream.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/seekablestream/SeekablePathStream.java' -> `./src/main/java/htsjdk/samtools/seekablestream/SeekablePathStream.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/seekablestream/SeekableStream.java' -> `./src/main/java/htsjdk/samtools/seekablestream/SeekableStream.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/fastq/FastqWriterFactory.java' -> `./src/main/java/htsjdk/samtools/fastq/FastqWriterFactory.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/fastq/AsyncFastqWriter.java' -> `./src/main/java/htsjdk/samtools/fastq/AsyncFastqWriter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/fastq/FastqEncoder.java' -> `./src/main/java/htsjdk/samtools/fastq/FastqEncoder.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/fastq/BasicFastqWriter.java' -> `./src/main/java/htsjdk/samtools/fastq/BasicFastqWriter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/fastq/FastqRecord.java' -> `./src/main/java/htsjdk/samtools/fastq/FastqRecord.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/fastq/FastqConstants.java' -> `./src/main/java/htsjdk/samtools/fastq/FastqConstants.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/fastq/FastqReader.java' -> `./src/main/java/htsjdk/samtools/fastq/FastqReader.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/samtools/fastq/FastqWriter.java' -> `./src/main/java/htsjdk/samtools/fastq/FastqWriter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/BinaryFeatureCodec.java' -> `./src/main/java/htsjdk/tribble/BinaryFeatureCodec.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/FeatureReader.java' -> `./src/main/java/htsjdk/tribble/FeatureReader.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/TribbleIndexedFeatureReader.java' -> `./src/main/java/htsjdk/tribble/TribbleIndexedFeatureReader.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/AbstractFeatureReader.java' -> `./src/main/java/htsjdk/tribble/AbstractFeatureReader.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/readme.txt' -> `./src/main/java/htsjdk/tribble/readme.txt'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/TabixFeatureReader.java' -> `./src/main/java/htsjdk/tribble/TabixFeatureReader.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/SimpleFeature.java' -> `./src/main/java/htsjdk/tribble/SimpleFeature.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/FeatureCodec.java' -> `./src/main/java/htsjdk/tribble/FeatureCodec.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/NameAwareCodec.java' -> `./src/main/java/htsjdk/tribble/NameAwareCodec.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/AbstractFeatureCodec.java' -> `./src/main/java/htsjdk/tribble/AbstractFeatureCodec.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/FeatureCodecHeader.java' -> `./src/main/java/htsjdk/tribble/FeatureCodecHeader.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/TribbleException.java' -> `./src/main/java/htsjdk/tribble/TribbleException.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/Feature.java' -> `./src/main/java/htsjdk/tribble/Feature.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/CloseableTribbleIterator.java' -> `./src/main/java/htsjdk/tribble/CloseableTribbleIterator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/Tribble.java' -> `./src/main/java/htsjdk/tribble/Tribble.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/AsciiFeatureCodec.java' -> `./src/main/java/htsjdk/tribble/AsciiFeatureCodec.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/readers/TabixIteratorLineReader.java' -> `./src/main/java/htsjdk/tribble/readers/TabixIteratorLineReader.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/readers/SynchronousLineReader.java' -> `./src/main/java/htsjdk/tribble/readers/SynchronousLineReader.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/readers/LongLineBufferedReader.java' -> `./src/main/java/htsjdk/tribble/readers/LongLineBufferedReader.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/readers/LineIteratorImpl.java' -> `./src/main/java/htsjdk/tribble/readers/LineIteratorImpl.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/readers/AsciiLineReader.java' -> `./src/main/java/htsjdk/tribble/readers/AsciiLineReader.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/readers/LineIterator.java' -> `./src/main/java/htsjdk/tribble/readers/LineIterator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/readers/PositionalBufferedStream.java' -> `./src/main/java/htsjdk/tribble/readers/PositionalBufferedStream.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/readers/Positional.java' -> `./src/main/java/htsjdk/tribble/readers/Positional.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/readers/LineReader.java' -> `./src/main/java/htsjdk/tribble/readers/LineReader.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/readers/TabixReader.java' -> `./src/main/java/htsjdk/tribble/readers/TabixReader.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/readers/AsciiLineReaderIterator.java' -> `./src/main/java/htsjdk/tribble/readers/AsciiLineReaderIterator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/bed/BEDCodec.java' -> `./src/main/java/htsjdk/tribble/bed/BEDCodec.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/bed/BEDFeature.java' -> `./src/main/java/htsjdk/tribble/bed/BEDFeature.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/bed/FullBEDFeature.java' -> `./src/main/java/htsjdk/tribble/bed/FullBEDFeature.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/bed/SimpleBEDFeature.java' -> `./src/main/java/htsjdk/tribble/bed/SimpleBEDFeature.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/exception/CodecLineParsingException.java' -> `./src/main/java/htsjdk/tribble/exception/CodecLineParsingException.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/exception/UnsortedFileException.java' -> `./src/main/java/htsjdk/tribble/exception/UnsortedFileException.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/util/MathUtils.java' -> `./src/main/java/htsjdk/tribble/util/MathUtils.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/util/ParsingUtils.java' -> `./src/main/java/htsjdk/tribble/util/ParsingUtils.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/util/LittleEndianOutputStream.java' -> `./src/main/java/htsjdk/tribble/util/LittleEndianOutputStream.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/util/URLHelper.java' -> `./src/main/java/htsjdk/tribble/util/URLHelper.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/util/RemoteURLHelper.java' -> `./src/main/java/htsjdk/tribble/util/RemoteURLHelper.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/util/FTPHelper.java' -> `./src/main/java/htsjdk/tribble/util/FTPHelper.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/util/HTTPHelper.java' -> `./src/main/java/htsjdk/tribble/util/HTTPHelper.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/util/TabixUtils.java' -> `./src/main/java/htsjdk/tribble/util/TabixUtils.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/util/LittleEndianInputStream.java' -> `./src/main/java/htsjdk/tribble/util/LittleEndianInputStream.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/util/ftp/.gitignore' -> `./src/main/java/htsjdk/tribble/util/ftp/.gitignore'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/util/popgen/HardyWeinbergCalculation.java' -> `./src/main/java/htsjdk/tribble/util/popgen/HardyWeinbergCalculation.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/annotation/Strand.java' -> `./src/main/java/htsjdk/tribble/annotation/Strand.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/example/IndicesAreEqual.java' -> `./src/main/java/htsjdk/tribble/example/IndicesAreEqual.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/example/ExampleBinaryCodec.java' -> `./src/main/java/htsjdk/tribble/example/ExampleBinaryCodec.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/example/ProfileIndexReading.java' -> `./src/main/java/htsjdk/tribble/example/ProfileIndexReading.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/example/IndexToTable.java' -> `./src/main/java/htsjdk/tribble/example/IndexToTable.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/example/CountRecords.java' -> `./src/main/java/htsjdk/tribble/example/CountRecords.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/index/IndexCreator.java' -> `./src/main/java/htsjdk/tribble/index/IndexCreator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/index/ChrIndex.java' -> `./src/main/java/htsjdk/tribble/index/ChrIndex.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/index/DynamicIndexCreator.java' -> `./src/main/java/htsjdk/tribble/index/DynamicIndexCreator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/index/Index.java' -> `./src/main/java/htsjdk/tribble/index/Index.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/index/AbstractIndex.java' -> `./src/main/java/htsjdk/tribble/index/AbstractIndex.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/index/Block.java' -> `./src/main/java/htsjdk/tribble/index/Block.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/index/TribbleIndexCreator.java' -> `./src/main/java/htsjdk/tribble/index/TribbleIndexCreator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/index/MutableIndex.java' -> `./src/main/java/htsjdk/tribble/index/MutableIndex.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/index/IndexFactory.java' -> `./src/main/java/htsjdk/tribble/index/IndexFactory.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/index/interval/IntervalIndexCreator.java' -> `./src/main/java/htsjdk/tribble/index/interval/IntervalIndexCreator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/index/interval/IntervalTree.java' -> `./src/main/java/htsjdk/tribble/index/interval/IntervalTree.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/index/interval/Interval.java' -> `./src/main/java/htsjdk/tribble/index/interval/Interval.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/index/interval/IntervalTreeIndex.java' -> `./src/main/java/htsjdk/tribble/index/interval/IntervalTreeIndex.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/index/linear/LinearIndex.java' -> `./src/main/java/htsjdk/tribble/index/linear/LinearIndex.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/index/linear/LinearIndexCreator.java' -> `./src/main/java/htsjdk/tribble/index/linear/LinearIndexCreator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/index/tabix/TabixFormat.java' -> `./src/main/java/htsjdk/tribble/index/tabix/TabixFormat.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/index/tabix/TabixIndex.java' -> `./src/main/java/htsjdk/tribble/index/tabix/TabixIndex.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/tribble/index/tabix/TabixIndexCreator.java' -> `./src/main/java/htsjdk/tribble/index/tabix/TabixIndexCreator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/utils/SAMSequenceDictionaryExtractor.java' -> `./src/main/java/htsjdk/variant/utils/SAMSequenceDictionaryExtractor.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/utils/GeneralUtils.java' -> `./src/main/java/htsjdk/variant/utils/GeneralUtils.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/vcf/VCFConstants.java' -> `./src/main/java/htsjdk/variant/vcf/VCFConstants.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/vcf/VCFStandardHeaderLines.java' -> `./src/main/java/htsjdk/variant/vcf/VCFStandardHeaderLines.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/vcf/VCFContigHeaderLine.java' -> `./src/main/java/htsjdk/variant/vcf/VCFContigHeaderLine.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/vcf/VCFHeaderLineTranslator.java' -> `./src/main/java/htsjdk/variant/vcf/VCFHeaderLineTranslator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/vcf/VCFHeaderVersion.java' -> `./src/main/java/htsjdk/variant/vcf/VCFHeaderVersion.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/vcf/VCFHeaderLineType.java' -> `./src/main/java/htsjdk/variant/vcf/VCFHeaderLineType.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/vcf/VCFHeader.java' -> `./src/main/java/htsjdk/variant/vcf/VCFHeader.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/vcf/VCFFilterHeaderLine.java' -> `./src/main/java/htsjdk/variant/vcf/VCFFilterHeaderLine.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/vcf/VCFIDHeaderLine.java' -> `./src/main/java/htsjdk/variant/vcf/VCFIDHeaderLine.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/vcf/VCFSimpleHeaderLine.java' -> `./src/main/java/htsjdk/variant/vcf/VCFSimpleHeaderLine.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/vcf/VCFEncoder.java' -> `./src/main/java/htsjdk/variant/vcf/VCFEncoder.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/vcf/VCFFormatHeaderLine.java' -> `./src/main/java/htsjdk/variant/vcf/VCFFormatHeaderLine.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/vcf/VCFFileReader.java' -> `./src/main/java/htsjdk/variant/vcf/VCFFileReader.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/vcf/AbstractVCFCodec.java' -> `./src/main/java/htsjdk/variant/vcf/AbstractVCFCodec.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/vcf/VCFRecordCodec.java' -> `./src/main/java/htsjdk/variant/vcf/VCFRecordCodec.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/vcf/VCFUtils.java' -> `./src/main/java/htsjdk/variant/vcf/VCFUtils.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/vcf/VCFCompoundHeaderLine.java' -> `./src/main/java/htsjdk/variant/vcf/VCFCompoundHeaderLine.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/vcf/VCF3Codec.java' -> `./src/main/java/htsjdk/variant/vcf/VCF3Codec.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/vcf/VCFInfoHeaderLine.java' -> `./src/main/java/htsjdk/variant/vcf/VCFInfoHeaderLine.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/vcf/VCFHeaderLine.java' -> `./src/main/java/htsjdk/variant/vcf/VCFHeaderLine.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/vcf/VCFCodec.java' -> `./src/main/java/htsjdk/variant/vcf/VCFCodec.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/vcf/VCFHeaderLineCount.java' -> `./src/main/java/htsjdk/variant/vcf/VCFHeaderLineCount.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/bcf2/BCF2Codec.java' -> `./src/main/java/htsjdk/variant/bcf2/BCF2Codec.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/bcf2/BCF2Type.java' -> `./src/main/java/htsjdk/variant/bcf2/BCF2Type.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/bcf2/BCF2Utils.java' -> `./src/main/java/htsjdk/variant/bcf2/BCF2Utils.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders.java' -> `./src/main/java/htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/bcf2/BCF2LazyGenotypesDecoder.java' -> `./src/main/java/htsjdk/variant/bcf2/BCF2LazyGenotypesDecoder.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/bcf2/BCF2Decoder.java' -> `./src/main/java/htsjdk/variant/bcf2/BCF2Decoder.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/bcf2/BCFVersion.java' -> `./src/main/java/htsjdk/variant/bcf2/BCFVersion.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/example/PrintVariantsExample.java' -> `./src/main/java/htsjdk/variant/example/PrintVariantsExample.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/variantcontext/VariantContextUtils.java' -> `./src/main/java/htsjdk/variant/variantcontext/VariantContextUtils.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/variantcontext/GenotypeBuilder.java' -> `./src/main/java/htsjdk/variant/variantcontext/GenotypeBuilder.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/variantcontext/GenotypeType.java' -> `./src/main/java/htsjdk/variant/variantcontext/GenotypeType.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/variantcontext/StructuralVariantType.java' -> `./src/main/java/htsjdk/variant/variantcontext/StructuralVariantType.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/variantcontext/VariantJEXLContext.java' -> `./src/main/java/htsjdk/variant/variantcontext/VariantJEXLContext.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/variantcontext/FastGenotype.java' -> `./src/main/java/htsjdk/variant/variantcontext/FastGenotype.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/variantcontext/GenotypeJEXLContext.java' -> `./src/main/java/htsjdk/variant/variantcontext/GenotypeJEXLContext.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/variantcontext/CommonInfo.java' -> `./src/main/java/htsjdk/variant/variantcontext/CommonInfo.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/variantcontext/VariantContextComparator.java' -> `./src/main/java/htsjdk/variant/variantcontext/VariantContextComparator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/variantcontext/LazyGenotypesContext.java' -> `./src/main/java/htsjdk/variant/variantcontext/LazyGenotypesContext.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/variantcontext/GenotypesContext.java' -> `./src/main/java/htsjdk/variant/variantcontext/GenotypesContext.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/variantcontext/JEXLMap.java' -> `./src/main/java/htsjdk/variant/variantcontext/JEXLMap.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/variantcontext/Genotype.java' -> `./src/main/java/htsjdk/variant/variantcontext/Genotype.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/variantcontext/Allele.java' -> `./src/main/java/htsjdk/variant/variantcontext/Allele.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/variantcontext/VariantContext.java' -> `./src/main/java/htsjdk/variant/variantcontext/VariantContext.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/variantcontext/VariantContextBuilder.java' -> `./src/main/java/htsjdk/variant/variantcontext/VariantContextBuilder.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/variantcontext/GenotypeLikelihoods.java' -> `./src/main/java/htsjdk/variant/variantcontext/GenotypeLikelihoods.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/variantcontext/JexlMissingValueTreatment.java' -> `./src/main/java/htsjdk/variant/variantcontext/JexlMissingValueTreatment.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/variantcontext/filter/JavascriptVariantFilter.java' -> `./src/main/java/htsjdk/variant/variantcontext/filter/JavascriptVariantFilter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/variantcontext/filter/FilteringVariantContextIterator.java' -> `./src/main/java/htsjdk/variant/variantcontext/filter/FilteringVariantContextIterator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/variantcontext/filter/VariantContextFilter.java' -> `./src/main/java/htsjdk/variant/variantcontext/filter/VariantContextFilter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/variantcontext/filter/CompoundFilter.java' -> `./src/main/java/htsjdk/variant/variantcontext/filter/CompoundFilter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/variantcontext/filter/PassingVariantFilter.java' -> `./src/main/java/htsjdk/variant/variantcontext/filter/PassingVariantFilter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/variantcontext/filter/SnpFilter.java' -> `./src/main/java/htsjdk/variant/variantcontext/filter/SnpFilter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/variantcontext/filter/HeterozygosityFilter.java' -> `./src/main/java/htsjdk/variant/variantcontext/filter/HeterozygosityFilter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/variantcontext/filter/GenotypeQualityFilter.java' -> `./src/main/java/htsjdk/variant/variantcontext/filter/GenotypeQualityFilter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/variantcontext/filter/FilteringIterator.java' -> `./src/main/java/htsjdk/variant/variantcontext/filter/FilteringIterator.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/variantcontext/writer/BCF2FieldWriterManager.java' -> `./src/main/java/htsjdk/variant/variantcontext/writer/BCF2FieldWriterManager.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/variantcontext/writer/VariantContextWriter.java' -> `./src/main/java/htsjdk/variant/variantcontext/writer/VariantContextWriter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/variantcontext/writer/SortingVariantContextWriterBase.java' -> `./src/main/java/htsjdk/variant/variantcontext/writer/SortingVariantContextWriterBase.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/variantcontext/writer/AsyncVariantContextWriter.java' -> `./src/main/java/htsjdk/variant/variantcontext/writer/AsyncVariantContextWriter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/variantcontext/writer/VCFWriter.java' -> `./src/main/java/htsjdk/variant/variantcontext/writer/VCFWriter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/variantcontext/writer/BCF2Encoder.java' -> `./src/main/java/htsjdk/variant/variantcontext/writer/BCF2Encoder.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/variantcontext/writer/BCF2Writer.java' -> `./src/main/java/htsjdk/variant/variantcontext/writer/BCF2Writer.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/variantcontext/writer/IndexingVariantContextWriter.java' -> `./src/main/java/htsjdk/variant/variantcontext/writer/IndexingVariantContextWriter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/variantcontext/writer/Options.java' -> `./src/main/java/htsjdk/variant/variantcontext/writer/Options.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.java' -> `./src/main/java/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/variantcontext/writer/SortingVariantContextWriter.java' -> `./src/main/java/htsjdk/variant/variantcontext/writer/SortingVariantContextWriter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/variantcontext/writer/VariantContextWriterBuilder.java' -> `./src/main/java/htsjdk/variant/variantcontext/writer/VariantContextWriterBuilder.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.java' -> `./src/main/java/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/main/java/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.java' -> `./src/main/java/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/testng.xml' -> `./src/test/resources/testng.xml'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/s_1_1101.filter' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/s_1_1101.filter'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C11.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C11.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C9.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C9.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C16.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C16.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C59.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C59.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C25.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C25.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C60.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C60.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C2.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C2.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C41.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C41.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C57.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C57.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C32.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C32.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C33.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C33.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C56.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C56.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C50.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C50.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C3.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C3.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C14.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C14.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C19.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C19.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C45.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C45.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C30.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C30.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C36.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C36.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C26.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C26.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C48.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C48.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C53.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C53.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C12.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C12.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C43.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C43.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C34.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C34.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C46.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C46.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C20.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C20.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C44.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C44.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C28.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C28.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C10.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C10.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C27.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C27.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C29.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C29.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C37.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C37.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C64.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C64.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C61.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C61.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C7.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C7.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C18.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C18.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C38.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C38.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C13.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C13.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C42.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C42.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C8.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C8.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C62.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C62.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C22.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C22.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C55.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C55.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C49.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C49.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C65.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C65.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C15.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C15.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C40.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C40.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C5.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C5.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C23.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C23.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C58.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C58.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C6.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C6.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C31.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C31.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C1.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C1.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C63.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C63.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C66.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C66.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C35.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C35.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C52.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C52.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C54.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C54.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C17.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C17.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C39.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C39.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C4.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C4.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C51.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C51.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C21.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C21.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C24.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C24.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C47.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C47.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/L001/s_1_1101.clocs' -> `./src/test/resources/net/sf/picard/illumina/125T125T/Data/Intensities/L001/s_1_1101.clocs'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/s_1_1101.filter' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/s_1_1101.filter'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C11.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C11.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C9.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C9.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C16.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C16.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C25.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C25.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C2.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C2.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C41.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C41.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C57.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C57.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C32.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C32.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C33.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C33.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C56.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C56.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C50.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C50.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C3.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C3.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C14.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C14.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C19.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C19.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C45.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C45.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C30.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C30.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C36.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C36.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C26.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C26.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C48.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C48.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C53.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C53.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C12.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C12.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C43.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C43.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C34.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C34.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C46.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C46.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C20.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C20.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C44.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C44.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C28.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C28.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C10.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C10.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C27.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C27.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C29.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C29.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C37.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C37.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C7.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C7.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C18.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C18.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C38.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C38.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C13.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C13.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C42.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C42.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C8.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C8.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C22.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C22.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C55.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C55.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C49.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C49.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C15.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C15.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C40.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C40.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C5.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C5.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C23.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C23.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C58.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C58.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C6.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C6.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C31.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C31.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C1.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C1.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C35.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C35.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C52.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C52.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C54.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C54.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C17.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C17.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C39.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C39.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C4.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C4.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C51.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C51.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C21.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C21.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C24.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C24.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C47.1/s_1_1101.bcl' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C47.1/s_1_1101.bcl'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/sams/GACCAGGA.sam' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/sams/GACCAGGA.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/sams/CTGTAATC.sam' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/sams/CTGTAATC.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/sams/ATTATCAA.sam' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/sams/ATTATCAA.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/sams/CGCTATGT.sam' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/sams/CGCTATGT.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/sams/N.sam' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/sams/N.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/sams/ACAGTTGA.sam' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/sams/ACAGTTGA.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/sams/TGTAATCA.sam' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/sams/TGTAATCA.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/sams/ACAGGTAT.sam' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/sams/ACAGGTAT.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/sams/CAATAGTC.sam' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/sams/CAATAGTC.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/sams/TGCAAGTA.sam' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/sams/TGCAAGTA.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/sams/AGGTCGCA.sam' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/sams/AGGTCGCA.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/sams/CAGCGGTA.sam' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/sams/CAGCGGTA.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/sams/ACTAAGAC.sam' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/sams/ACTAAGAC.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/sams/GCCTAGCC.sam' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/sams/GCCTAGCC.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/net/sf/picard/illumina/25T8B25T/sams/GCCGTCGA.sam' -> `./src/test/resources/net/sf/picard/illumina/25T8B25T/sams/GCCGTCGA.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/tribble/tmp/.gitignore' -> `./src/test/resources/tribble/tmp/.gitignore'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/block_compressed.sam.gz' -> `./src/test/resources/htsjdk/samtools/block_compressed.sam.gz'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/compressed.bam' -> `./src/test/resources/htsjdk/samtools/compressed.bam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/unsorted.sam' -> `./src/test/resources/htsjdk/samtools/unsorted.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/issue76.bam.bai' -> `./src/test/resources/htsjdk/samtools/issue76.bam.bai'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/serialization_test.bam' -> `./src/test/resources/htsjdk/samtools/serialization_test.bam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/hg19mini.fasta.fai' -> `./src/test/resources/htsjdk/samtools/hg19mini.fasta.fai'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram_tlen.fasta' -> `./src/test/resources/htsjdk/samtools/cram_tlen.fasta'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/sequenceWithSpace.bam' -> `./src/test/resources/htsjdk/samtools/sequenceWithSpace.bam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/compressed.sam.gz' -> `./src/test/resources/htsjdk/samtools/compressed.sam.gz'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/hg19mini.fasta' -> `./src/test/resources/htsjdk/samtools/hg19mini.fasta'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram_with_bai_index.cram.bai' -> `./src/test/resources/htsjdk/samtools/cram_with_bai_index.cram.bai'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/readWithBadRname.sam' -> `./src/test/resources/htsjdk/samtools/readWithBadRname.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/issue76.bam' -> `./src/test/resources/htsjdk/samtools/issue76.bam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram_with_crai_index.cram.crai' -> `./src/test/resources/htsjdk/samtools/cram_with_crai_index.cram.crai'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/inttest.sam' -> `./src/test/resources/htsjdk/samtools/inttest.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/roundtrip.sam' -> `./src/test/resources/htsjdk/samtools/roundtrip.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/noheader.sam' -> `./src/test/resources/htsjdk/samtools/noheader.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram_query_sorted.fasta' -> `./src/test/resources/htsjdk/samtools/cram_query_sorted.fasta'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/coordinate_sorted.sam' -> `./src/test/resources/htsjdk/samtools/coordinate_sorted.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram_query_sorted.cram' -> `./src/test/resources/htsjdk/samtools/cram_query_sorted.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/empty_no_empty_gzip_block.bai' -> `./src/test/resources/htsjdk/samtools/empty_no_empty_gzip_block.bai'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/uncompressed.sam' -> `./src/test/resources/htsjdk/samtools/uncompressed.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/queryname_sorted.sam' -> `./src/test/resources/htsjdk/samtools/queryname_sorted.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/samFilter01.js' -> `./src/test/resources/htsjdk/samtools/samFilter01.js'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/serialization_test.sam' -> `./src/test/resources/htsjdk/samtools/serialization_test.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram_tlen_reads.sorted.sam' -> `./src/test/resources/htsjdk/samtools/cram_tlen_reads.sorted.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/inttest.bam' -> `./src/test/resources/htsjdk/samtools/inttest.bam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/empty.bam' -> `./src/test/resources/htsjdk/samtools/empty.bam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram_with_bai_index.cram' -> `./src/test/resources/htsjdk/samtools/cram_with_bai_index.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/serialization_test.bam.bai' -> `./src/test/resources/htsjdk/samtools/serialization_test.bam.bai'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/empty_no_empty_gzip_block.bam' -> `./src/test/resources/htsjdk/samtools/empty_no_empty_gzip_block.bam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram_query_sorted.fasta.fai' -> `./src/test/resources/htsjdk/samtools/cram_query_sorted.fasta.fai'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/hg19mini.dict' -> `./src/test/resources/htsjdk/samtools/hg19mini.dict'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/empty.bai' -> `./src/test/resources/htsjdk/samtools/empty.bai'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/samFilter02.js' -> `./src/test/resources/htsjdk/samtools/samFilter02.js'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram_with_crai_index.cram' -> `./src/test/resources/htsjdk/samtools/cram_with_crai_index.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/sequenceWithSpace.sam' -> `./src/test/resources/htsjdk/samtools/sequenceWithSpace.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram_tlen.fasta.fai' -> `./src/test/resources/htsjdk/samtools/cram_tlen.fasta.fai'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/sra/test_archive.sra' -> `./src/test/resources/htsjdk/samtools/sra/test_archive.sra'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/io/empty.txt' -> `./src/test/resources/htsjdk/samtools/io/empty.txt'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/io/slurptest.txt' -> `./src/test/resources/htsjdk/samtools/io/slurptest.txt'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/io/5newline5.txt' -> `./src/test/resources/htsjdk/samtools/io/5newline5.txt'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/BAMCigarOverflowTest/CigarOverflowTest.bam' -> `./src/test/resources/htsjdk/samtools/BAMCigarOverflowTest/CigarOverflowTest.bam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/util/whitespace_text_file.txt' -> `./src/test/resources/htsjdk/samtools/util/whitespace_text_file.txt'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/util/defective_bgzf.bam' -> `./src/test/resources/htsjdk/samtools/util/defective_bgzf.bam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/util/random.bin' -> `./src/test/resources/htsjdk/samtools/util/random.bin'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/util/no_bgzf_terminator.bam' -> `./src/test/resources/htsjdk/samtools/util/no_bgzf_terminator.bam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/util/random.bin.gz' -> `./src/test/resources/htsjdk/samtools/util/random.bin.gz'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/util/QualityEncodingDetectorTest/illumina-as-standard.bam' -> `./src/test/resources/htsjdk/samtools/util/QualityEncodingDetectorTest/illumina-as-standard.bam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/util/QualityEncodingDetectorTest/5k-30BB2AAXX.3.aligned.sam.fastq' -> `./src/test/resources/htsjdk/samtools/util/QualityEncodingDetectorTest/5k-30BB2AAXX.3.aligned.sam.fastq'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/util/QualityEncodingDetectorTest/s_1_sequence.txt' -> `./src/test/resources/htsjdk/samtools/util/QualityEncodingDetectorTest/s_1_sequence.txt'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/util/QualityEncodingDetectorTest/unmapped.sam' -> `./src/test/resources/htsjdk/samtools/util/QualityEncodingDetectorTest/unmapped.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/util/QualityEncodingDetectorTest/solexa-as-standard.bam' -> `./src/test/resources/htsjdk/samtools/util/QualityEncodingDetectorTest/solexa-as-standard.bam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/util/QualityEncodingDetectorTest/solexa_full_range_as_solexa.fastq' -> `./src/test/resources/htsjdk/samtools/util/QualityEncodingDetectorTest/solexa_full_range_as_solexa.fastq'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/SAMIntegerTagTest/variousAttributes.bam' -> `./src/test/resources/htsjdk/samtools/SAMIntegerTagTest/variousAttributes.bam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/SAMIntegerTagTest/variousAttributes.sam' -> `./src/test/resources/htsjdk/samtools/SAMIntegerTagTest/variousAttributes.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/reference/crlf.fasta.fai' -> `./src/test/resources/htsjdk/samtools/reference/crlf.fasta.fai'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz.gzi' -> `./src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz.gzi'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta.fai' -> `./src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta.fai'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/reference/header_with_white_space.fasta' -> `./src/test/resources/htsjdk/samtools/reference/header_with_white_space.fasta'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.fasta.fai' -> `./src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.fasta.fai'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta' -> `./src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.noindex.fasta' -> `./src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.noindex.fasta'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/reference/crlf.fasta' -> `./src/test/resources/htsjdk/samtools/reference/crlf.fasta'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.fai' -> `./src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.fai'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz' -> `./src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/reference/header_with_white_space.fasta.fai' -> `./src/test/resources/htsjdk/samtools/reference/header_with_white_space.fasta.fai'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/reference/reference_with_trailing_whitespace.dict' -> `./src/test/resources/htsjdk/samtools/reference/reference_with_trailing_whitespace.dict'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/reference/testing.fai' -> `./src/test/resources/htsjdk/samtools/reference/testing.fai'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/reference/reference_with_trailing_whitespace.fasta' -> `./src/test/resources/htsjdk/samtools/reference/reference_with_trailing_whitespace.fasta'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz.fai' -> `./src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz.fai'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta' -> `./src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.dict' -> `./src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.dict'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/intervallist/IntervalListFromVCFTestComp.interval_list' -> `./src/test/resources/htsjdk/samtools/intervallist/IntervalListFromVCFTestComp.interval_list'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/intervallist/IntervalListFromVCFTestCompInverse.interval_list' -> `./src/test/resources/htsjdk/samtools/intervallist/IntervalListFromVCFTestCompInverse.interval_list'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/intervallist/IntervalListFromVCFTestManual.vcf' -> `./src/test/resources/htsjdk/samtools/intervallist/IntervalListFromVCFTestManual.vcf'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/intervallist/IntervalListchr123_empty.interval_list' -> `./src/test/resources/htsjdk/samtools/intervallist/IntervalListchr123_empty.interval_list'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/intervallist/IntervalListFromVCFTestManualComp.interval_list' -> `./src/test/resources/htsjdk/samtools/intervallist/IntervalListFromVCFTestManualComp.interval_list'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/intervallist/IntervalListFromVCFTestCompInverseManual.interval_list' -> `./src/test/resources/htsjdk/samtools/intervallist/IntervalListFromVCFTestCompInverseManual.interval_list'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/intervallist/IntervalListFromVCFTest.vcf' -> `./src/test/resources/htsjdk/samtools/intervallist/IntervalListFromVCFTest.vcf'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/liftover/hg18ToHg19.over.chain' -> `./src/test/resources/htsjdk/samtools/liftover/hg18ToHg19.over.chain'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam' -> `./src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_with_index.bam.bai' -> `./src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_with_index.bam.bai'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam' -> `./src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_with_index.bam' -> `./src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_with_index.bam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai' -> `./src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/metrics/metricsOneCopy.metrics' -> `./src/test/resources/htsjdk/samtools/metrics/metricsOneCopy.metrics'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/metrics/metricsOneModifiedHistogram.metrics' -> `./src/test/resources/htsjdk/samtools/metrics/metricsOneModifiedHistogram.metrics'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/metrics/metricsOneModifiedMetrics.metrics' -> `./src/test/resources/htsjdk/samtools/metrics/metricsOneModifiedMetrics.metrics'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/metrics/metricsOne.metrics' -> `./src/test/resources/htsjdk/samtools/metrics/metricsOne.metrics'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta' -> `./src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/xx#large_aux.2.1.cram' -> `./src/test/resources/htsjdk/samtools/cram/xx#large_aux.2.1.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/c1#pad2.3.0.cram' -> `./src/test/resources/htsjdk/samtools/cram/c1#pad2.3.0.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/ce#supp.sam' -> `./src/test/resources/htsjdk/samtools/cram/ce#supp.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/auxf#values.3.0.cram' -> `./src/test/resources/htsjdk/samtools/cram/auxf#values.3.0.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/xx#rg.sam' -> `./src/test/resources/htsjdk/samtools/cram/xx#rg.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/auxf.fa.fai' -> `./src/test/resources/htsjdk/samtools/cram/auxf.fa.fai'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/ce#tag_padded.3.0.cram' -> `./src/test/resources/htsjdk/samtools/cram/ce#tag_padded.3.0.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram.bai' -> `./src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram.bai'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/ce#unmap2.sam' -> `./src/test/resources/htsjdk/samtools/cram/ce#unmap2.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/c1#bounds.3.0.cram' -> `./src/test/resources/htsjdk/samtools/cram/c1#bounds.3.0.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/ce#unmap.3.0.cram' -> `./src/test/resources/htsjdk/samtools/cram/ce#unmap.3.0.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/c1#pad2.2.1.cram' -> `./src/test/resources/htsjdk/samtools/cram/c1#pad2.2.1.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/c1#noseq.2.1.cram' -> `./src/test/resources/htsjdk/samtools/cram/c1#noseq.2.1.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/xx#large_aux.sam' -> `./src/test/resources/htsjdk/samtools/cram/xx#large_aux.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/ce#large_seq.2.1.cram' -> `./src/test/resources/htsjdk/samtools/cram/ce#large_seq.2.1.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/ce#large_seq.sam' -> `./src/test/resources/htsjdk/samtools/cram/ce#large_seq.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/test2.cram' -> `./src/test/resources/htsjdk/samtools/cram/test2.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/xx#minimal.2.1.cram' -> `./src/test/resources/htsjdk/samtools/cram/xx#minimal.2.1.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/ce#5b.2.1.cram' -> `./src/test/resources/htsjdk/samtools/cram/ce#5b.2.1.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/xx#blank.sam' -> `./src/test/resources/htsjdk/samtools/cram/xx#blank.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/ce#unmap1.2.1.cram' -> `./src/test/resources/htsjdk/samtools/cram/ce#unmap1.2.1.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/c1#pad3.2.1.cram' -> `./src/test/resources/htsjdk/samtools/cram/c1#pad3.2.1.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/ce#1.3.0.cram' -> `./src/test/resources/htsjdk/samtools/cram/ce#1.3.0.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/xx#tlen.2.1.cram' -> `./src/test/resources/htsjdk/samtools/cram/xx#tlen.2.1.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/ce#5b.sam' -> `./src/test/resources/htsjdk/samtools/cram/ce#5b.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram' -> `./src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/NA12878.20.21.1-100.100-SeqsPerSlice.500-unMapped.cram.crai' -> `./src/test/resources/htsjdk/samtools/cram/NA12878.20.21.1-100.100-SeqsPerSlice.500-unMapped.cram.crai'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/cramQueryTestEmpty.cram' -> `./src/test/resources/htsjdk/samtools/cram/cramQueryTestEmpty.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/ce#large_seq.3.0.cram' -> `./src/test/resources/htsjdk/samtools/cram/ce#large_seq.3.0.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram' -> `./src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/auxf.alteredForMD5test.fa.fai' -> `./src/test/resources/htsjdk/samtools/cram/auxf.alteredForMD5test.fa.fai'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/ce#5.3.0.cram' -> `./src/test/resources/htsjdk/samtools/cram/ce#5.3.0.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/NA12878.20.21.1-100.100-SeqsPerSlice.0-unMapped.cram.crai' -> `./src/test/resources/htsjdk/samtools/cram/NA12878.20.21.1-100.100-SeqsPerSlice.0-unMapped.cram.crai'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/ce#1.sam' -> `./src/test/resources/htsjdk/samtools/cram/ce#1.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta.fai' -> `./src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta.fai'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/xx#unsorted.3.0.cram' -> `./src/test/resources/htsjdk/samtools/cram/xx#unsorted.3.0.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/ce#unmap1.3.0.cram' -> `./src/test/resources/htsjdk/samtools/cram/ce#unmap1.3.0.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.1-100.dict' -> `./src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.1-100.dict'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/xx#pair.2.1.cram' -> `./src/test/resources/htsjdk/samtools/cram/xx#pair.2.1.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/ce#tag_depadded.3.0.cram' -> `./src/test/resources/htsjdk/samtools/cram/ce#tag_depadded.3.0.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/ce#1.2.1.cram' -> `./src/test/resources/htsjdk/samtools/cram/ce#1.2.1.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.subset.dict' -> `./src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.subset.dict'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.dict' -> `./src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.dict'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/ce#supp.2.1.cram' -> `./src/test/resources/htsjdk/samtools/cram/ce#supp.2.1.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/xx#large_aux2.sam' -> `./src/test/resources/htsjdk/samtools/cram/xx#large_aux2.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/xx#rg.3.0.cram' -> `./src/test/resources/htsjdk/samtools/cram/xx#rg.3.0.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/test.cram' -> `./src/test/resources/htsjdk/samtools/cram/test.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/c1#noseq.3.0.cram' -> `./src/test/resources/htsjdk/samtools/cram/c1#noseq.3.0.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/c1#bounds.sam' -> `./src/test/resources/htsjdk/samtools/cram/c1#bounds.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/c1#pad3.3.0.cram' -> `./src/test/resources/htsjdk/samtools/cram/c1#pad3.3.0.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/xx.fa.fai' -> `./src/test/resources/htsjdk/samtools/cram/xx.fa.fai'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/auxf.alteredForMD5test.fa' -> `./src/test/resources/htsjdk/samtools/cram/auxf.alteredForMD5test.fa'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/c1#pad1.sam' -> `./src/test/resources/htsjdk/samtools/cram/c1#pad1.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/ce#2.sam' -> `./src/test/resources/htsjdk/samtools/cram/ce#2.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/c1#clip.2.1.cram' -> `./src/test/resources/htsjdk/samtools/cram/c1#clip.2.1.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/c2#pad.3.0.cram' -> `./src/test/resources/htsjdk/samtools/cram/c2#pad.3.0.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/ce#unmap.sam' -> `./src/test/resources/htsjdk/samtools/cram/ce#unmap.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/xx#large_aux2.3.0.cram' -> `./src/test/resources/htsjdk/samtools/cram/xx#large_aux2.3.0.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/c1#pad3.sam' -> `./src/test/resources/htsjdk/samtools/cram/c1#pad3.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/NA12878.20.21.1-100.100-SeqsPerSlice.500-unMapped.cram' -> `./src/test/resources/htsjdk/samtools/cram/NA12878.20.21.1-100.100-SeqsPerSlice.500-unMapped.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/ce#tag_padded.sam' -> `./src/test/resources/htsjdk/samtools/cram/ce#tag_padded.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram.bai' -> `./src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram.bai'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/ce#tag_padded.2.1.cram' -> `./src/test/resources/htsjdk/samtools/cram/ce#tag_padded.2.1.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/xx#minimal.3.0.cram' -> `./src/test/resources/htsjdk/samtools/cram/xx#minimal.3.0.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/c1#unknown.2.1.cram' -> `./src/test/resources/htsjdk/samtools/cram/c1#unknown.2.1.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/ce.fa.fai' -> `./src/test/resources/htsjdk/samtools/cram/ce.fa.fai'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/xx#triplet.sam' -> `./src/test/resources/htsjdk/samtools/cram/xx#triplet.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/c1#pad2.sam' -> `./src/test/resources/htsjdk/samtools/cram/c1#pad2.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/xx#pair.3.0.cram' -> `./src/test/resources/htsjdk/samtools/cram/xx#pair.3.0.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/test.cram.bai' -> `./src/test/resources/htsjdk/samtools/cram/test.cram.bai'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/ce#unmap1.sam' -> `./src/test/resources/htsjdk/samtools/cram/ce#unmap1.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/c1#unknown.3.0.cram' -> `./src/test/resources/htsjdk/samtools/cram/c1#unknown.3.0.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/xx#tlen.3.0.cram' -> `./src/test/resources/htsjdk/samtools/cram/xx#tlen.3.0.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/xx#large_aux.3.0.cram' -> `./src/test/resources/htsjdk/samtools/cram/xx#large_aux.3.0.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.subset.fasta.fai' -> `./src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.subset.fasta.fai'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/xx#blank.3.0.cram' -> `./src/test/resources/htsjdk/samtools/cram/xx#blank.3.0.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/ce#tag_depadded.2.1.cram' -> `./src/test/resources/htsjdk/samtools/cram/ce#tag_depadded.2.1.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/ce#5.2.1.cram' -> `./src/test/resources/htsjdk/samtools/cram/ce#5.2.1.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/auxf#values.sam' -> `./src/test/resources/htsjdk/samtools/cram/auxf#values.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/xx#large_aux2.2.1.cram' -> `./src/test/resources/htsjdk/samtools/cram/xx#large_aux2.2.1.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/NA12878.20.21.1-100.100-SeqsPerSlice.1-unMapped.cram.crai' -> `./src/test/resources/htsjdk/samtools/cram/NA12878.20.21.1-100.100-SeqsPerSlice.1-unMapped.cram.crai'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/c1.fa' -> `./src/test/resources/htsjdk/samtools/cram/c1.fa'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/c2#pad.2.1.cram' -> `./src/test/resources/htsjdk/samtools/cram/c2#pad.2.1.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/c1#pad1.3.0.cram' -> `./src/test/resources/htsjdk/samtools/cram/c1#pad1.3.0.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/auxf#values.2.1.cram' -> `./src/test/resources/htsjdk/samtools/cram/auxf#values.2.1.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/ce#2.3.0.cram' -> `./src/test/resources/htsjdk/samtools/cram/ce#2.3.0.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/ce#2.2.1.cram' -> `./src/test/resources/htsjdk/samtools/cram/ce#2.2.1.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/auxf.fa' -> `./src/test/resources/htsjdk/samtools/cram/auxf.fa'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/ce#unmap.2.1.cram' -> `./src/test/resources/htsjdk/samtools/cram/ce#unmap.2.1.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/xx#rg.2.1.cram' -> `./src/test/resources/htsjdk/samtools/cram/xx#rg.2.1.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/ce#5.sam' -> `./src/test/resources/htsjdk/samtools/cram/ce#5.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/ce#5b.3.0.cram' -> `./src/test/resources/htsjdk/samtools/cram/ce#5b.3.0.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/xx#tlen2.2.1.cram' -> `./src/test/resources/htsjdk/samtools/cram/xx#tlen2.2.1.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/xx#unsorted.sam' -> `./src/test/resources/htsjdk/samtools/cram/xx#unsorted.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/xx#tlen2.3.0.cram' -> `./src/test/resources/htsjdk/samtools/cram/xx#tlen2.3.0.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/cramQueryWithCRAI.cram' -> `./src/test/resources/htsjdk/samtools/cram/cramQueryWithCRAI.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/ce#unmap2.2.1.cram' -> `./src/test/resources/htsjdk/samtools/cram/ce#unmap2.2.1.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/cramQueryTestEmpty.cram.bai' -> `./src/test/resources/htsjdk/samtools/cram/cramQueryTestEmpty.cram.bai'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.1-100.fasta.fai' -> `./src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.1-100.fasta.fai'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/c1.fa.fai' -> `./src/test/resources/htsjdk/samtools/cram/c1.fa.fai'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.1-100.fasta' -> `./src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.1-100.fasta'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/xx#triplet.2.1.cram' -> `./src/test/resources/htsjdk/samtools/cram/xx#triplet.2.1.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/ce#supp.3.0.cram' -> `./src/test/resources/htsjdk/samtools/cram/ce#supp.3.0.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/c1#clip.3.0.cram' -> `./src/test/resources/htsjdk/samtools/cram/c1#clip.3.0.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/ce#tag_depadded.sam' -> `./src/test/resources/htsjdk/samtools/cram/ce#tag_depadded.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/xx#blank.2.1.cram' -> `./src/test/resources/htsjdk/samtools/cram/xx#blank.2.1.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/cramQueryWithCRAI.cram.crai' -> `./src/test/resources/htsjdk/samtools/cram/cramQueryWithCRAI.cram.crai'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/xx#minimal.sam' -> `./src/test/resources/htsjdk/samtools/cram/xx#minimal.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/xx.fa' -> `./src/test/resources/htsjdk/samtools/cram/xx.fa'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/c1#bounds.2.1.cram' -> `./src/test/resources/htsjdk/samtools/cram/c1#bounds.2.1.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/ce#unmap2.3.0.cram' -> `./src/test/resources/htsjdk/samtools/cram/ce#unmap2.3.0.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/CEUTrio.HiSeq.WGS.b37.NA12878.20.first.8000.bam' -> `./src/test/resources/htsjdk/samtools/cram/CEUTrio.HiSeq.WGS.b37.NA12878.20.first.8000.bam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/c1#clip.sam' -> `./src/test/resources/htsjdk/samtools/cram/c1#clip.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/NA12878.20.21.1-100.100-SeqsPerSlice.0-unMapped.cram' -> `./src/test/resources/htsjdk/samtools/cram/NA12878.20.21.1-100.100-SeqsPerSlice.0-unMapped.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/xx#pair.sam' -> `./src/test/resources/htsjdk/samtools/cram/xx#pair.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/c1#pad1.2.1.cram' -> `./src/test/resources/htsjdk/samtools/cram/c1#pad1.2.1.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/xx#triplet.3.0.cram' -> `./src/test/resources/htsjdk/samtools/cram/xx#triplet.3.0.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/ce.fa' -> `./src/test/resources/htsjdk/samtools/cram/ce.fa'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/c1#unknown.sam' -> `./src/test/resources/htsjdk/samtools/cram/c1#unknown.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/xx#unsorted.2.1.cram' -> `./src/test/resources/htsjdk/samtools/cram/xx#unsorted.2.1.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/NA12878.20.21.1-100.100-SeqsPerSlice.1-unMapped.cram' -> `./src/test/resources/htsjdk/samtools/cram/NA12878.20.21.1-100.100-SeqsPerSlice.1-unMapped.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.subset.fasta' -> `./src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.subset.fasta'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/c1#noseq.sam' -> `./src/test/resources/htsjdk/samtools/cram/c1#noseq.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/CRAMException/testContigNotInRef.fasta' -> `./src/test/resources/htsjdk/samtools/cram/CRAMException/testContigNotInRef.fasta'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/CRAMException/testContigNotInRef.fa.fai' -> `./src/test/resources/htsjdk/samtools/cram/CRAMException/testContigNotInRef.fa.fai'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/CRAMException/testContigNotInRef.cram.bai' -> `./src/test/resources/htsjdk/samtools/cram/CRAMException/testContigNotInRef.cram.bai'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/CRAMException/testContigNotInRef.dict' -> `./src/test/resources/htsjdk/samtools/cram/CRAMException/testContigNotInRef.dict'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/CRAMException/testContigNotInRef.cram' -> `./src/test/resources/htsjdk/samtools/cram/CRAMException/testContigNotInRef.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/CRAMException/testContigNotInRef.fa' -> `./src/test/resources/htsjdk/samtools/cram/CRAMException/testContigNotInRef.fa'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/cram/io/bzip2-test.bz2' -> `./src/test/resources/htsjdk/samtools/cram/io/bzip2-test.bz2'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/seekablestream/megabyteZeros.dat' -> `./src/test/resources/htsjdk/samtools/seekablestream/megabyteZeros.dat'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/seekablestream/seekTest.txt' -> `./src/test/resources/htsjdk/samtools/seekablestream/seekTest.txt'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/ValidateSamFileTest/test_samfile_version_1pt5.bam' -> `./src/test/resources/htsjdk/samtools/ValidateSamFileTest/test_samfile_version_1pt5.bam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/ValidateSamFileTest/nm_tag_validation.fa' -> `./src/test/resources/htsjdk/samtools/ValidateSamFileTest/nm_tag_validation.fa'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/ValidateSamFileTest/duplicated_reads_out_of_order.sam' -> `./src/test/resources/htsjdk/samtools/ValidateSamFileTest/duplicated_reads_out_of_order.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/ValidateSamFileTest/invalid_coord_sort_order.sam' -> `./src/test/resources/htsjdk/samtools/ValidateSamFileTest/invalid_coord_sort_order.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/ValidateSamFileTest/truncated_tag.sam' -> `./src/test/resources/htsjdk/samtools/ValidateSamFileTest/truncated_tag.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/ValidateSamFileTest/bad_index.bai' -> `./src/test/resources/htsjdk/samtools/ValidateSamFileTest/bad_index.bai'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/ValidateSamFileTest/missing_platform_unit.sam' -> `./src/test/resources/htsjdk/samtools/ValidateSamFileTest/missing_platform_unit.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/ValidateSamFileTest/inappropriate_mate_cigar_string.sam' -> `./src/test/resources/htsjdk/samtools/ValidateSamFileTest/inappropriate_mate_cigar_string.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/ValidateSamFileTest/hanging_tab.sam' -> `./src/test/resources/htsjdk/samtools/ValidateSamFileTest/hanging_tab.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/ValidateSamFileTest/zero_length_read.sam' -> `./src/test/resources/htsjdk/samtools/ValidateSamFileTest/zero_length_read.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/ValidateSamFileTest/invalid_queryname_sort_order.sam' -> `./src/test/resources/htsjdk/samtools/ValidateSamFileTest/invalid_queryname_sort_order.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/ValidateSamFileTest/nm_tag_validation.cram' -> `./src/test/resources/htsjdk/samtools/ValidateSamFileTest/nm_tag_validation.cram'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/ValidateSamFileTest/invalid_mate_cigar_string.sam' -> `./src/test/resources/htsjdk/samtools/ValidateSamFileTest/invalid_mate_cigar_string.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/ValidateSamFileTest/buggyHeader.sam' -> `./src/test/resources/htsjdk/samtools/ValidateSamFileTest/buggyHeader.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/ValidateSamFileTest/mate_cigar_and_oqs.sam' -> `./src/test/resources/htsjdk/samtools/ValidateSamFileTest/mate_cigar_and_oqs.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/ValidateSamFileTest/duplicate_rg.sam' -> `./src/test/resources/htsjdk/samtools/ValidateSamFileTest/duplicate_rg.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/ValidateSamFileTest/nm_tag_validation.fa.fai' -> `./src/test/resources/htsjdk/samtools/ValidateSamFileTest/nm_tag_validation.fa.fai'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/ValidateSamFileTest/invalid_platform_unit.sam' -> `./src/test/resources/htsjdk/samtools/ValidateSamFileTest/invalid_platform_unit.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/ValidateSamFileTest/mate_cigar_and_no_oqs.sam' -> `./src/test/resources/htsjdk/samtools/ValidateSamFileTest/mate_cigar_and_no_oqs.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/ValidateSamFileTest/missing_fields.sam' -> `./src/test/resources/htsjdk/samtools/ValidateSamFileTest/missing_fields.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/ValidateSamFileTest/bad_index.bam' -> `./src/test/resources/htsjdk/samtools/ValidateSamFileTest/bad_index.bam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/ValidateSamFileTest/duplicated_reads.sam' -> `./src/test/resources/htsjdk/samtools/ValidateSamFileTest/duplicated_reads.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/ValidateSamFileTest/valid.sam' -> `./src/test/resources/htsjdk/samtools/ValidateSamFileTest/valid.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/ValidateSamFileTest/truncated_quals.sam' -> `./src/test/resources/htsjdk/samtools/ValidateSamFileTest/truncated_quals.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/ValidateSamFileTest/truncated.bam' -> `./src/test/resources/htsjdk/samtools/ValidateSamFileTest/truncated.bam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/Chromosome5to9.bam' -> `./src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/Chromosome5to9.bam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/Chromosome1to10.bam' -> `./src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/Chromosome1to10.bam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/case1/chr11sub_file2.sam' -> `./src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/case1/chr11sub_file2.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/case1/chr11sub_file1.sam' -> `./src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/case1/chr11sub_file1.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/case1/expected_output.sam' -> `./src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/case1/expected_output.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/unsorted_input/2.sam' -> `./src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/unsorted_input/2.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/unsorted_input/1.sam' -> `./src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/unsorted_input/1.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/case2/chr11sub_file2.sam' -> `./src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/case2/chr11sub_file2.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/case2/chr11sub_file1.sam' -> `./src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/case2/chr11sub_file1.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/case2/expected_output.sam' -> `./src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/case2/expected_output.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/case2/chr11sub_file3.sam' -> `./src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/case2/chr11sub_file3.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/case2/chr11sub_file4.sam' -> `./src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/case2/chr11sub_file4.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/SequenceUtil/reference_with_lower_and_uppercase.dict' -> `./src/test/resources/htsjdk/samtools/SequenceUtil/reference_with_lower_and_uppercase.dict'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/SequenceUtil/reference_with_lower_and_uppercase.fasta' -> `./src/test/resources/htsjdk/samtools/SequenceUtil/reference_with_lower_and_uppercase.fasta'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/SequenceUtil/reference_with_lower_and_uppercase.fasta.fai' -> `./src/test/resources/htsjdk/samtools/SequenceUtil/reference_with_lower_and_uppercase.fasta.fai'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/samtools/SequenceUtil/upper_and_lowercase_read.sam' -> `./src/test/resources/htsjdk/samtools/SequenceUtil/upper_and_lowercase_read.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/test.gff' -> `./src/test/resources/htsjdk/tribble/test.gff'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/large.txt' -> `./src/test/resources/htsjdk/tribble/large.txt'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/test.vcf.gz' -> `./src/test/resources/htsjdk/tribble/test.vcf.gz'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/test with spaces.vcf' -> `./src/test/resources/htsjdk/tribble/test with spaces.vcf'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/Tb.vcf.idx' -> `./src/test/resources/htsjdk/tribble/Tb.vcf.idx'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/trioDup.vcf' -> `./src/test/resources/htsjdk/tribble/trioDup.vcf'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/trio.vcf.idx' -> `./src/test/resources/htsjdk/tribble/trio.vcf.idx'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/vcfexample.vcf.gz' -> `./src/test/resources/htsjdk/tribble/vcfexample.vcf.gz'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/test.tabix.bed.gz' -> `./src/test/resources/htsjdk/tribble/test.tabix.bed.gz'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/trio.vcf' -> `./src/test/resources/htsjdk/tribble/trio.vcf'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/basicDbSNP.dbsnp' -> `./src/test/resources/htsjdk/tribble/basicDbSNP.dbsnp'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/complexExample.vcf' -> `./src/test/resources/htsjdk/tribble/complexExample.vcf'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/vcfexample.vcf' -> `./src/test/resources/htsjdk/tribble/vcfexample.vcf'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/testIntervalList.list' -> `./src/test/resources/htsjdk/tribble/testIntervalList.list'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/vcfexample.vcf.truncated.hdr.gz' -> `./src/test/resources/htsjdk/tribble/vcfexample.vcf.truncated.hdr.gz'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/testGeliText.txt' -> `./src/test/resources/htsjdk/tribble/testGeliText.txt'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/soapsnp.txt' -> `./src/test/resources/htsjdk/tribble/soapsnp.txt'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/fakeBed.bed' -> `./src/test/resources/htsjdk/tribble/fakeBed.bed'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/vcfexample.vcf.truncated.gz' -> `./src/test/resources/htsjdk/tribble/vcfexample.vcf.truncated.gz'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/fakeVCF.vcf.gz.tbi' -> `./src/test/resources/htsjdk/tribble/fakeVCF.vcf.gz.tbi'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/sites.bed' -> `./src/test/resources/htsjdk/tribble/sites.bed'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/vcfexample.vcf.gz.tbi' -> `./src/test/resources/htsjdk/tribble/vcfexample.vcf.gz.tbi'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/test.vcf' -> `./src/test/resources/htsjdk/tribble/test.vcf'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/fakeVCF.vcf.gz' -> `./src/test/resources/htsjdk/tribble/fakeVCF.vcf.gz'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/test.bed' -> `./src/test/resources/htsjdk/tribble/test.bed'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/test.tabix.bed.gz.tbi' -> `./src/test/resources/htsjdk/tribble/test.tabix.bed.gz.tbi'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/test.vcf.bgz' -> `./src/test/resources/htsjdk/tribble/test.vcf.bgz'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/bed/NA12878.deletions.10kbp.het.gq99.hand_curated.hg19.bed' -> `./src/test/resources/htsjdk/tribble/bed/NA12878.deletions.10kbp.het.gq99.hand_curated.hg19.bed'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/bed/NA12878.deletions.10kbp.het.gq99.hand_curated.hg19_fixed.bed' -> `./src/test/resources/htsjdk/tribble/bed/NA12878.deletions.10kbp.het.gq99.hand_curated.hg19_fixed.bed'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/bed/Unigene.sample.bed' -> `./src/test/resources/htsjdk/tribble/bed/Unigene.sample.bed'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/bed/disconcontigs.bed' -> `./src/test/resources/htsjdk/tribble/bed/disconcontigs.bed'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/bed/unsorted.bed' -> `./src/test/resources/htsjdk/tribble/bed/unsorted.bed'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/tmp/.gitignore' -> `./src/test/resources/htsjdk/tribble/tmp/.gitignore'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/index/chrY_Y4_small.bed' -> `./src/test/resources/htsjdk/tribble/index/chrY_Y4_small.bed'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/tabix/trioDup.vcf' -> `./src/test/resources/htsjdk/tribble/tabix/trioDup.vcf'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/tabix/trioDup.vcf.gz.tbi' -> `./src/test/resources/htsjdk/tribble/tabix/trioDup.vcf.gz.tbi'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/tabix/trioDup.vcf.gz' -> `./src/test/resources/htsjdk/tribble/tabix/trioDup.vcf.gz'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/tabix/YRI.trio.2010_07.indel.sites.vcf.gz.tbi' -> `./src/test/resources/htsjdk/tribble/tabix/YRI.trio.2010_07.indel.sites.vcf.gz.tbi'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/tabix/testTabixIndex.vcf' -> `./src/test/resources/htsjdk/tribble/tabix/testTabixIndex.vcf'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/tabix/bigger.vcf.gz.tbi' -> `./src/test/resources/htsjdk/tribble/tabix/bigger.vcf.gz.tbi'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/tabix/YRI.trio.2010_07.indel.sites.vcf.gz' -> `./src/test/resources/htsjdk/tribble/tabix/YRI.trio.2010_07.indel.sites.vcf.gz'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/tabix/testTabixIndex.vcf.gz' -> `./src/test/resources/htsjdk/tribble/tabix/testTabixIndex.vcf.gz'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/AbstractFeatureReaderTest/baseVariants.vcf.gz.tbi' -> `./src/test/resources/htsjdk/tribble/AbstractFeatureReaderTest/baseVariants.vcf.gz.tbi'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/AbstractFeatureReaderTest/baseVariants.vcf.idx' -> `./src/test/resources/htsjdk/tribble/AbstractFeatureReaderTest/baseVariants.vcf.idx'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/AbstractFeatureReaderTest/mangledBaseVariants.vcf' -> `./src/test/resources/htsjdk/tribble/AbstractFeatureReaderTest/mangledBaseVariants.vcf'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/AbstractFeatureReaderTest/baseVariants.vcf' -> `./src/test/resources/htsjdk/tribble/AbstractFeatureReaderTest/baseVariants.vcf'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/AbstractFeatureReaderTest/baseVariants.mangled.vcf.gz' -> `./src/test/resources/htsjdk/tribble/AbstractFeatureReaderTest/baseVariants.mangled.vcf.gz'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/AbstractFeatureReaderTest/mangledBaseVariants.vcf.idx' -> `./src/test/resources/htsjdk/tribble/AbstractFeatureReaderTest/mangledBaseVariants.vcf.idx'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/AbstractFeatureReaderTest/baseVariants.mangled.vcf.gz.tbi' -> `./src/test/resources/htsjdk/tribble/AbstractFeatureReaderTest/baseVariants.mangled.vcf.gz.tbi'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/AbstractFeatureReaderTest/baseVariants.vcf.gz' -> `./src/test/resources/htsjdk/tribble/AbstractFeatureReaderTest/baseVariants.vcf.gz'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/gwas/smallp.gwas' -> `./src/test/resources/htsjdk/tribble/gwas/smallp.gwas'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/split/test.bin.split' -> `./src/test/resources/htsjdk/tribble/split/test.bin.split'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/split/test.bin.part2' -> `./src/test/resources/htsjdk/tribble/split/test.bin.part2'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/split/test.bin.part1' -> `./src/test/resources/htsjdk/tribble/split/test.bin.part1'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/tribble/split/test.bin.part3' -> `./src/test/resources/htsjdk/tribble/split/test.bin.part3'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/variant/serialization_test.bcf.idx' -> `./src/test/resources/htsjdk/variant/serialization_test.bcf.idx'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/variant/breakpoint.vcf' -> `./src/test/resources/htsjdk/variant/breakpoint.vcf'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/variant/serialization_test.bcf' -> `./src/test/resources/htsjdk/variant/serialization_test.bcf'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/variant/ex2.bgzf.bcf.csi' -> `./src/test/resources/htsjdk/variant/ex2.bgzf.bcf.csi'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/variant/VQSR.mixedTest.recal' -> `./src/test/resources/htsjdk/variant/VQSR.mixedTest.recal'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/variant/ex2.vcf' -> `./src/test/resources/htsjdk/variant/ex2.vcf'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/variant/dbsnp_135.b37.1000.vcf' -> `./src/test/resources/htsjdk/variant/dbsnp_135.b37.1000.vcf'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/variant/VCF4HeaderTest.vcf' -> `./src/test/resources/htsjdk/variant/VCF4HeaderTest.vcf'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/variant/variantFilter01.js' -> `./src/test/resources/htsjdk/variant/variantFilter01.js'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/variant/structuralvariants.vcf' -> `./src/test/resources/htsjdk/variant/structuralvariants.vcf'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/variant/ILLUMINA.wex.broad_phase2_baseline.20111114.both.exome.genotypes.1000.vcf' -> `./src/test/resources/htsjdk/variant/ILLUMINA.wex.broad_phase2_baseline.20111114.both.exome.genotypes.1000.vcf'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/variant/variantFilter02.js' -> `./src/test/resources/htsjdk/variant/variantFilter02.js'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/variant/HiSeq.10000.vcf' -> `./src/test/resources/htsjdk/variant/HiSeq.10000.vcf'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/variant/diagnosis_targets_testfile.vcf' -> `./src/test/resources/htsjdk/variant/diagnosis_targets_testfile.vcf'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/variant/utils/SamSequenceDictionaryExtractor/test1.dict' -> `./src/test/resources/htsjdk/variant/utils/SamSequenceDictionaryExtractor/test1.dict'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/variant/utils/SamSequenceDictionaryExtractor/test1_comp.interval_list' -> `./src/test/resources/htsjdk/variant/utils/SamSequenceDictionaryExtractor/test1_comp.interval_list'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/variant/utils/SamSequenceDictionaryExtractor/test1.vcf' -> `./src/test/resources/htsjdk/variant/utils/SamSequenceDictionaryExtractor/test1.vcf'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/variant/utils/SamSequenceDictionaryExtractor/test4_comp.interval_list' -> `./src/test/resources/htsjdk/variant/utils/SamSequenceDictionaryExtractor/test4_comp.interval_list'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/variant/utils/SamSequenceDictionaryExtractor/test2_comp.interval_list' -> `./src/test/resources/htsjdk/variant/utils/SamSequenceDictionaryExtractor/test2_comp.interval_list'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/variant/utils/SamSequenceDictionaryExtractor/Homo_sapiens_assembly18.trimmed.fasta.fai' -> `./src/test/resources/htsjdk/variant/utils/SamSequenceDictionaryExtractor/Homo_sapiens_assembly18.trimmed.fasta.fai'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/variant/utils/SamSequenceDictionaryExtractor/test1.vcf.idx' -> `./src/test/resources/htsjdk/variant/utils/SamSequenceDictionaryExtractor/test1.vcf.idx'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/variant/utils/SamSequenceDictionaryExtractor/Homo_sapiens_assembly18.trimmed.fasta' -> `./src/test/resources/htsjdk/variant/utils/SamSequenceDictionaryExtractor/Homo_sapiens_assembly18.trimmed.fasta'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/variant/utils/SamSequenceDictionaryExtractor/empty.interval_list' -> `./src/test/resources/htsjdk/variant/utils/SamSequenceDictionaryExtractor/empty.interval_list'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/variant/utils/SamSequenceDictionaryExtractor/Homo_sapiens_assembly18.trimmed.dict' -> `./src/test/resources/htsjdk/variant/utils/SamSequenceDictionaryExtractor/Homo_sapiens_assembly18.trimmed.dict'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/variant/utils/SamSequenceDictionaryExtractor/ScreenSamReads.100.input.sam' -> `./src/test/resources/htsjdk/variant/utils/SamSequenceDictionaryExtractor/ScreenSamReads.100.input.sam'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/resources/htsjdk/variant/utils/SamSequenceDictionaryExtractor/test3_comp.interval_list' -> `./src/test/resources/htsjdk/variant/utils/SamSequenceDictionaryExtractor/test3_comp.interval_list'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/HtsjdkTest.java' -> `./src/test/java/htsjdk/HtsjdkTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/DuplicateSetIteratorTest.java' -> `./src/test/java/htsjdk/samtools/DuplicateSetIteratorTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/SamFlagFieldTest.java' -> `./src/test/java/htsjdk/samtools/SamFlagFieldTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/SamHeaderRecordComparatorTest.java' -> `./src/test/java/htsjdk/samtools/SamHeaderRecordComparatorTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/BAMIteratorTest.java' -> `./src/test/java/htsjdk/samtools/BAMIteratorTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/AbstractBAMFileIndexTest.java' -> `./src/test/java/htsjdk/samtools/AbstractBAMFileIndexTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/SamReaderFactoryTest.java' -> `./src/test/java/htsjdk/samtools/SamReaderFactoryTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/SAMRecordDuplicateComparatorTest.java' -> `./src/test/java/htsjdk/samtools/SAMRecordDuplicateComparatorTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/CRAMContainerStreamWriterTest.java' -> `./src/test/java/htsjdk/samtools/CRAMContainerStreamWriterTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/CRAMFileWriterTest.java' -> `./src/test/java/htsjdk/samtools/CRAMFileWriterTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/SamFileHeaderMergerTest.java' -> `./src/test/java/htsjdk/samtools/SamFileHeaderMergerTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/DownsamplingIteratorTests.java' -> `./src/test/java/htsjdk/samtools/DownsamplingIteratorTests.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/BAMFileWriterTest.java' -> `./src/test/java/htsjdk/samtools/BAMFileWriterTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/CRAMIndexQueryTest.java' -> `./src/test/java/htsjdk/samtools/CRAMIndexQueryTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/CigarCodecTest.java' -> `./src/test/java/htsjdk/samtools/CigarCodecTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/SamReaderTest.java' -> `./src/test/java/htsjdk/samtools/SamReaderTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/MergingSamRecordIteratorGroupCollisionTest.java' -> `./src/test/java/htsjdk/samtools/MergingSamRecordIteratorGroupCollisionTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/CRAMFileWriterWithIndexTest.java' -> `./src/test/java/htsjdk/samtools/CRAMFileWriterWithIndexTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/BAMIndexWriterTest.java' -> `./src/test/java/htsjdk/samtools/BAMIndexWriterTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/SeekableByteChannelFromBuffer.java' -> `./src/test/java/htsjdk/samtools/SeekableByteChannelFromBuffer.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/GenomicIndexUtilTest.java' -> `./src/test/java/htsjdk/samtools/GenomicIndexUtilTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/BAMFileIndexTest.java' -> `./src/test/java/htsjdk/samtools/BAMFileIndexTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/SAMSequenceRecordTest.java' -> `./src/test/java/htsjdk/samtools/SAMSequenceRecordTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/SamPairUtilTest.java' -> `./src/test/java/htsjdk/samtools/SamPairUtilTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/CRAMBAIIndexerTest.java' -> `./src/test/java/htsjdk/samtools/CRAMBAIIndexerTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/BAMQueryMultipleIntervalsIteratorFilterTest.java' -> `./src/test/java/htsjdk/samtools/BAMQueryMultipleIntervalsIteratorFilterTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/SamStreamsTest.java' -> `./src/test/java/htsjdk/samtools/SamStreamsTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/PathInputResourceTest.java' -> `./src/test/java/htsjdk/samtools/PathInputResourceTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/SamReaderSortTest.java' -> `./src/test/java/htsjdk/samtools/SamReaderSortTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/BinTest.java' -> `./src/test/java/htsjdk/samtools/BinTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/CRAMFileReaderTest.java' -> `./src/test/java/htsjdk/samtools/CRAMFileReaderTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/SAMProgramRecordTest.java' -> `./src/test/java/htsjdk/samtools/SAMProgramRecordTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/CRAMFileBAIIndexTest.java' -> `./src/test/java/htsjdk/samtools/CRAMFileBAIIndexTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/BAMCigarOverflowTest.java' -> `./src/test/java/htsjdk/samtools/BAMCigarOverflowTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/CRAMFileCRAIIndexTest.java' -> `./src/test/java/htsjdk/samtools/CRAMFileCRAIIndexTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/SAMReadGroupRecordTest.java' -> `./src/test/java/htsjdk/samtools/SAMReadGroupRecordTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/SAMTextWriterTest.java' -> `./src/test/java/htsjdk/samtools/SAMTextWriterTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java' -> `./src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/CigarTest.java' -> `./src/test/java/htsjdk/samtools/CigarTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/CRAMCRAIIndexerTest.java' -> `./src/test/java/htsjdk/samtools/CRAMCRAIIndexerTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/SequenceNameTruncationAndValidationTest.java' -> `./src/test/java/htsjdk/samtools/SequenceNameTruncationAndValidationTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/SAMSequenceDictionaryCodecTest.java' -> `./src/test/java/htsjdk/samtools/SAMSequenceDictionaryCodecTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/SAMTextReaderTest.java' -> `./src/test/java/htsjdk/samtools/SAMTextReaderTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/BAMRemoteFileTest.java' -> `./src/test/java/htsjdk/samtools/BAMRemoteFileTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/ProgramRecordChainingTest.java' -> `./src/test/java/htsjdk/samtools/ProgramRecordChainingTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/SamIndexesTest.java' -> `./src/test/java/htsjdk/samtools/SamIndexesTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/MergingSamRecordIteratorTest.java' -> `./src/test/java/htsjdk/samtools/MergingSamRecordIteratorTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/CRAMComplianceTest.java' -> `./src/test/java/htsjdk/samtools/CRAMComplianceTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/SAMFlagTest.java' -> `./src/test/java/htsjdk/samtools/SAMFlagTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/SAMIntegerTagTest.java' -> `./src/test/java/htsjdk/samtools/SAMIntegerTagTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/SAMSequenceDictionaryTest.java' -> `./src/test/java/htsjdk/samtools/SAMSequenceDictionaryTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/SamSpecIntTest.java' -> `./src/test/java/htsjdk/samtools/SamSpecIntTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/SamFilesTest.java' -> `./src/test/java/htsjdk/samtools/SamFilesTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/SAMFileWriterFactoryTest.java' -> `./src/test/java/htsjdk/samtools/SAMFileWriterFactoryTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/ValidateSamFileTest.java' -> `./src/test/java/htsjdk/samtools/ValidateSamFileTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/ChunkTest.java' -> `./src/test/java/htsjdk/samtools/ChunkTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/SAMRecordUnitTest.java' -> `./src/test/java/htsjdk/samtools/SAMRecordUnitTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/BAMFileSpanTest.java' -> `./src/test/java/htsjdk/samtools/BAMFileSpanTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/CRAMEdgeCasesTest.java' -> `./src/test/java/htsjdk/samtools/CRAMEdgeCasesTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/SAMCloneTest.java' -> `./src/test/java/htsjdk/samtools/SAMCloneTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/SAMUtilsTest.java' -> `./src/test/java/htsjdk/samtools/SAMUtilsTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/sra/SRAQueryTest.java' -> `./src/test/java/htsjdk/samtools/sra/SRAQueryTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/sra/SRATest.java' -> `./src/test/java/htsjdk/samtools/sra/SRATest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/sra/SRAIndexTest.java' -> `./src/test/java/htsjdk/samtools/sra/SRAIndexTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/sra/SRAAccessionTest.java' -> `./src/test/java/htsjdk/samtools/sra/SRAAccessionTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/sra/AbstractSRATest.java' -> `./src/test/java/htsjdk/samtools/sra/AbstractSRATest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/sra/SRAReferenceTest.java' -> `./src/test/java/htsjdk/samtools/sra/SRAReferenceTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/sra/SRALazyRecordTest.java' -> `./src/test/java/htsjdk/samtools/sra/SRALazyRecordTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/util/StringLineReaderTest.java' -> `./src/test/java/htsjdk/samtools/util/StringLineReaderTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/util/SolexaQualityConverterTest.java' -> `./src/test/java/htsjdk/samtools/util/SolexaQualityConverterTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/util/AsyncBlockCompressedInputStreamTest.java' -> `./src/test/java/htsjdk/samtools/util/AsyncBlockCompressedInputStreamTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/util/AbstractLocusInfoTest.java' -> `./src/test/java/htsjdk/samtools/util/AbstractLocusInfoTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/util/IupacTest.java' -> `./src/test/java/htsjdk/samtools/util/IupacTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/util/Iso8601DateTest.java' -> `./src/test/java/htsjdk/samtools/util/Iso8601DateTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/util/DiskBackedQueueTest.java' -> `./src/test/java/htsjdk/samtools/util/DiskBackedQueueTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/util/IntervalTreeMapTest.java' -> `./src/test/java/htsjdk/samtools/util/IntervalTreeMapTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/util/RelativeIso8601DateTest.java' -> `./src/test/java/htsjdk/samtools/util/RelativeIso8601DateTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/util/EdgeReadIteratorTest.java' -> `./src/test/java/htsjdk/samtools/util/EdgeReadIteratorTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/util/CodeUtilTest.java' -> `./src/test/java/htsjdk/samtools/util/CodeUtilTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/util/BlockCompressedInputStreamTest.java' -> `./src/test/java/htsjdk/samtools/util/BlockCompressedInputStreamTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/util/IoUtilTest.java' -> `./src/test/java/htsjdk/samtools/util/IoUtilTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/util/MergingIteratorTest.java' -> `./src/test/java/htsjdk/samtools/util/MergingIteratorTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/util/AsyncBufferedIteratorTest.java' -> `./src/test/java/htsjdk/samtools/util/AsyncBufferedIteratorTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/util/PositionalOutputStreamTest.java' -> `./src/test/java/htsjdk/samtools/util/PositionalOutputStreamTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/util/BlockCompressedOutputStreamTest.java' -> `./src/test/java/htsjdk/samtools/util/BlockCompressedOutputStreamTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/util/BlockCompressedTerminatorTest.java' -> `./src/test/java/htsjdk/samtools/util/BlockCompressedTerminatorTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/util/ComparableTupleTest.java' -> `./src/test/java/htsjdk/samtools/util/ComparableTupleTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/util/BlockCompressedFilePointerUtilTest.java' -> `./src/test/java/htsjdk/samtools/util/BlockCompressedFilePointerUtilTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/util/SequenceUtilTest.java' -> `./src/test/java/htsjdk/samtools/util/SequenceUtilTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/util/HistogramTest.java' -> `./src/test/java/htsjdk/samtools/util/HistogramTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/util/CloseableIteratorTest.java' -> `./src/test/java/htsjdk/samtools/util/CloseableIteratorTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/util/AbstractRecordAndOffsetTest.java' -> `./src/test/java/htsjdk/samtools/util/AbstractRecordAndOffsetTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/util/BinaryCodecTest.java' -> `./src/test/java/htsjdk/samtools/util/BinaryCodecTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/util/CigarUtilTest.java' -> `./src/test/java/htsjdk/samtools/util/CigarUtilTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/util/CoordSpanInputSteamTest.java' -> `./src/test/java/htsjdk/samtools/util/CoordSpanInputSteamTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/util/DateParserTest.java' -> `./src/test/java/htsjdk/samtools/util/DateParserTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/util/SamLocusIteratorTest.java' -> `./src/test/java/htsjdk/samtools/util/SamLocusIteratorTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/util/QualityEncodingDetectorTest.java' -> `./src/test/java/htsjdk/samtools/util/QualityEncodingDetectorTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/util/OverlapDetectorTest.java' -> `./src/test/java/htsjdk/samtools/util/OverlapDetectorTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/util/TrimmingUtilTest.java' -> `./src/test/java/htsjdk/samtools/util/TrimmingUtilTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/util/SortingCollectionTest.java' -> `./src/test/java/htsjdk/samtools/util/SortingCollectionTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/util/IntervalTreeTest.java' -> `./src/test/java/htsjdk/samtools/util/IntervalTreeTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/util/EdgingRecordAndOffsetTest.java' -> `./src/test/java/htsjdk/samtools/util/EdgingRecordAndOffsetTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/util/TupleTest.java' -> `./src/test/java/htsjdk/samtools/util/TupleTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/util/CigarElementUnitTest.java' -> `./src/test/java/htsjdk/samtools/util/CigarElementUnitTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/util/IntervalListTest.java' -> `./src/test/java/htsjdk/samtools/util/IntervalListTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/util/SortingLongCollectionTest.java' -> `./src/test/java/htsjdk/samtools/util/SortingLongCollectionTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/util/AbstractLocusIteratorTestTemplate.java' -> `./src/test/java/htsjdk/samtools/util/AbstractLocusIteratorTestTemplate.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/util/AsyncWriterTest.java' -> `./src/test/java/htsjdk/samtools/util/AsyncWriterTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/apps/.gitignore' -> `./src/test/java/htsjdk/samtools/apps/.gitignore'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/filter/SolexaNoiseFilterTest.java' -> `./src/test/java/htsjdk/samtools/filter/SolexaNoiseFilterTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/filter/OverclippedReadFilterTest.java' -> `./src/test/java/htsjdk/samtools/filter/OverclippedReadFilterTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/filter/MappingQualityFilterTest.java' -> `./src/test/java/htsjdk/samtools/filter/MappingQualityFilterTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/filter/FailsVendorReadQualityFilterTest.java' -> `./src/test/java/htsjdk/samtools/filter/FailsVendorReadQualityFilterTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/filter/TagFilterTest.java' -> `./src/test/java/htsjdk/samtools/filter/TagFilterTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/filter/JavascriptSamRecordFilterTest.java' -> `./src/test/java/htsjdk/samtools/filter/JavascriptSamRecordFilterTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/filter/IntervalKeepPairFilterTest.java' -> `./src/test/java/htsjdk/samtools/filter/IntervalKeepPairFilterTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/filter/InsertSizeFilterTest.java' -> `./src/test/java/htsjdk/samtools/filter/InsertSizeFilterTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/reference/ReferenceSequenceFileFactoryTests.java' -> `./src/test/java/htsjdk/samtools/reference/ReferenceSequenceFileFactoryTests.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/reference/ReferenceSequenceFileWalkerTest.java' -> `./src/test/java/htsjdk/samtools/reference/ReferenceSequenceFileWalkerTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/reference/FakeReferenceSequenceFile.java' -> `./src/test/java/htsjdk/samtools/reference/FakeReferenceSequenceFile.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/reference/FastaSequenceIndexTest.java' -> `./src/test/java/htsjdk/samtools/reference/FastaSequenceIndexTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/reference/FastaSequenceFileTest.java' -> `./src/test/java/htsjdk/samtools/reference/FastaSequenceFileTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/reference/IndexedFastaSequenceFileTest.java' -> `./src/test/java/htsjdk/samtools/reference/IndexedFastaSequenceFileTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/reference/ReferenceSequenceTests.java' -> `./src/test/java/htsjdk/samtools/reference/ReferenceSequenceTests.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/reference/InMemoryReferenceSequenceFile.java' -> `./src/test/java/htsjdk/samtools/reference/InMemoryReferenceSequenceFile.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/reference/FastaSequenceIndexCreatorTest.java' -> `./src/test/java/htsjdk/samtools/reference/FastaSequenceIndexCreatorTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/liftover/LiftOverTest.java' -> `./src/test/java/htsjdk/samtools/liftover/LiftOverTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/metrics/VersionHeaderTest.java' -> `./src/test/java/htsjdk/samtools/metrics/VersionHeaderTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/metrics/MetricBaseTest.java' -> `./src/test/java/htsjdk/samtools/metrics/MetricBaseTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/metrics/MetricsFileTest.java' -> `./src/test/java/htsjdk/samtools/metrics/MetricsFileTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/metrics/StringHeaderTest.java' -> `./src/test/java/htsjdk/samtools/metrics/StringHeaderTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/cram/VersionTest.java' -> `./src/test/java/htsjdk/samtools/cram/VersionTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/cram/LosslessRoundTripTest.java' -> `./src/test/java/htsjdk/samtools/cram/LosslessRoundTripTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/cram/CRAIEntryTest.java' -> `./src/test/java/htsjdk/samtools/cram/CRAIEntryTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/cram/CRAIIndexTest.java' -> `./src/test/java/htsjdk/samtools/cram/CRAIIndexTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/cram/structure/SliceTests.java' -> `./src/test/java/htsjdk/samtools/cram/structure/SliceTests.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/cram/structure/CramCompressionRecordTest.java' -> `./src/test/java/htsjdk/samtools/cram/structure/CramCompressionRecordTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/cram/structure/ReadTagTest.java' -> `./src/test/java/htsjdk/samtools/cram/structure/ReadTagTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/cram/structure/SubstitutionMatrixTest.java' -> `./src/test/java/htsjdk/samtools/cram/structure/SubstitutionMatrixTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/cram/io/ITF8Test.java' -> `./src/test/java/htsjdk/samtools/cram/io/ITF8Test.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/cram/io/LTF8Test.java' -> `./src/test/java/htsjdk/samtools/cram/io/LTF8Test.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/cram/build/ContainerParserTest.java' -> `./src/test/java/htsjdk/samtools/cram/build/ContainerParserTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/cram/build/CramIOTest.java' -> `./src/test/java/htsjdk/samtools/cram/build/CramIOTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/cram/build/CompressionHeaderFactoryTest.java' -> `./src/test/java/htsjdk/samtools/cram/build/CompressionHeaderFactoryTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/cram/build/ContainerFactoryTest.java' -> `./src/test/java/htsjdk/samtools/cram/build/ContainerFactoryTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/cram/lossy/QualityScorePreservationTest.java' -> `./src/test/java/htsjdk/samtools/cram/lossy/QualityScorePreservationTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/cram/ref/EnaRefServiceTest.java' -> `./src/test/java/htsjdk/samtools/cram/ref/EnaRefServiceTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/cram/encoding/huffman/codec/HuffmanTest.java' -> `./src/test/java/htsjdk/samtools/cram/encoding/huffman/codec/HuffmanTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/cram/encoding/rans/RansTest.java' -> `./src/test/java/htsjdk/samtools/cram/encoding/rans/RansTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/seekablestream/SeekablePathStreamTest.java' -> `./src/test/java/htsjdk/samtools/seekablestream/SeekablePathStreamTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/seekablestream/SeekableFileStreamTest.java' -> `./src/test/java/htsjdk/samtools/seekablestream/SeekableFileStreamTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/seekablestream/SeekableStreamFactoryTest.java' -> `./src/test/java/htsjdk/samtools/seekablestream/SeekableStreamFactoryTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/seekablestream/SeekableMemoryStreamTest.java' -> `./src/test/java/htsjdk/samtools/seekablestream/SeekableMemoryStreamTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/seekablestream/SeekableFTPStreamTest.java' -> `./src/test/java/htsjdk/samtools/seekablestream/SeekableFTPStreamTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/seekablestream/SeekableBufferedStreamTest.java' -> `./src/test/java/htsjdk/samtools/seekablestream/SeekableBufferedStreamTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/fastq/FastqEncoderTest.java' -> `./src/test/java/htsjdk/samtools/fastq/FastqEncoderTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/fastq/FastqRecordTest.java' -> `./src/test/java/htsjdk/samtools/fastq/FastqRecordTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/samtools/fastq/.gitignore' -> `./src/test/java/htsjdk/samtools/fastq/.gitignore'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/tribble/TribbleIndexFeatureReaderTest.java' -> `./src/test/java/htsjdk/tribble/TribbleIndexFeatureReaderTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/tribble/TribbleTest.java' -> `./src/test/java/htsjdk/tribble/TribbleTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/tribble/AbstractFeatureReaderTest.java' -> `./src/test/java/htsjdk/tribble/AbstractFeatureReaderTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/tribble/TestUtils.java' -> `./src/test/java/htsjdk/tribble/TestUtils.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/tribble/BinaryFeaturesTest.java' -> `./src/test/java/htsjdk/tribble/BinaryFeaturesTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/tribble/FeatureReaderTest.java' -> `./src/test/java/htsjdk/tribble/FeatureReaderTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/tribble/readers/PositionalBufferedStreamTest.java' -> `./src/test/java/htsjdk/tribble/readers/PositionalBufferedStreamTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/tribble/readers/SynchronousLineReaderUnitTest.java' -> `./src/test/java/htsjdk/tribble/readers/SynchronousLineReaderUnitTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/tribble/readers/TabixReaderTest.java' -> `./src/test/java/htsjdk/tribble/readers/TabixReaderTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/tribble/readers/ReaderTest.java' -> `./src/test/java/htsjdk/tribble/readers/ReaderTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/tribble/readers/LongLineBufferedReaderTest.java' -> `./src/test/java/htsjdk/tribble/readers/LongLineBufferedReaderTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/tribble/readers/AsciiLineReaderTest.java' -> `./src/test/java/htsjdk/tribble/readers/AsciiLineReaderTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/tribble/bed/BEDCodecTest.java' -> `./src/test/java/htsjdk/tribble/bed/BEDCodecTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/tribble/util/ParsingUtilsTest.java' -> `./src/test/java/htsjdk/tribble/util/ParsingUtilsTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/tribble/util/ftp/FTPUtilsTest.java' -> `./src/test/java/htsjdk/tribble/util/ftp/FTPUtilsTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/tribble/util/ftp/FTPClientTest.java' -> `./src/test/java/htsjdk/tribble/util/ftp/FTPClientTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/tribble/util/popgen/HardyWeinbergCalculationTest.java' -> `./src/test/java/htsjdk/tribble/util/popgen/HardyWeinbergCalculationTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/tribble/index/IndexFactoryTest.java' -> `./src/test/java/htsjdk/tribble/index/IndexFactoryTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/tribble/index/IndexTest.java' -> `./src/test/java/htsjdk/tribble/index/IndexTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/tribble/index/interval/IntervalTreeTest.java' -> `./src/test/java/htsjdk/tribble/index/interval/IntervalTreeTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/tribble/index/linear/LinearIndexTest.java' -> `./src/test/java/htsjdk/tribble/index/linear/LinearIndexTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/tribble/index/tabix/TabixIndexTest.java' -> `./src/test/java/htsjdk/tribble/index/tabix/TabixIndexTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/tribble/source/.gitignore' -> `./src/test/java/htsjdk/tribble/source/.gitignore'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/variant/PrintVariantsExampleTest.java' -> `./src/test/java/htsjdk/variant/PrintVariantsExampleTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/variant/VariantBaseTest.java' -> `./src/test/java/htsjdk/variant/VariantBaseTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/variant/utils/SAMSequenceDictionaryExtractorTest.java' -> `./src/test/java/htsjdk/variant/utils/SAMSequenceDictionaryExtractorTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/variant/vcf/VCFHeaderLineTranslatorUnitTest.java' -> `./src/test/java/htsjdk/variant/vcf/VCFHeaderLineTranslatorUnitTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/variant/vcf/AbstractVCFCodecTest.java' -> `./src/test/java/htsjdk/variant/vcf/AbstractVCFCodecTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/variant/vcf/VCFCompoundHeaderLineUnitTest.java' -> `./src/test/java/htsjdk/variant/vcf/VCFCompoundHeaderLineUnitTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/variant/vcf/IndexFactoryUnitTest.java' -> `./src/test/java/htsjdk/variant/vcf/IndexFactoryUnitTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/variant/vcf/VCFHeaderLineUnitTest.java' -> `./src/test/java/htsjdk/variant/vcf/VCFHeaderLineUnitTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/variant/vcf/VCFEncoderTest.java' -> `./src/test/java/htsjdk/variant/vcf/VCFEncoderTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/variant/vcf/VCFHeaderUnitTest.java' -> `./src/test/java/htsjdk/variant/vcf/VCFHeaderUnitTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/variant/vcf/VCFStandardHeaderLinesUnitTest.java' -> `./src/test/java/htsjdk/variant/vcf/VCFStandardHeaderLinesUnitTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/variant/bcf2/BCF2EncoderDecoderUnitTest.java' -> `./src/test/java/htsjdk/variant/bcf2/BCF2EncoderDecoderUnitTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/variant/bcf2/BCF2UtilsUnitTest.java' -> `./src/test/java/htsjdk/variant/bcf2/BCF2UtilsUnitTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/variant/variantcontext/GenotypesContextUnitTest.java' -> `./src/test/java/htsjdk/variant/variantcontext/GenotypesContextUnitTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/variant/variantcontext/VariantContextTestProvider.java' -> `./src/test/java/htsjdk/variant/variantcontext/VariantContextTestProvider.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/variant/variantcontext/AlleleUnitTest.java' -> `./src/test/java/htsjdk/variant/variantcontext/AlleleUnitTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/variant/variantcontext/GenotypeBuilderTest.java' -> `./src/test/java/htsjdk/variant/variantcontext/GenotypeBuilderTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/variant/variantcontext/VariantContextBuilderTest.java' -> `./src/test/java/htsjdk/variant/variantcontext/VariantContextBuilderTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/variant/variantcontext/GenotypeUnitTest.java' -> `./src/test/java/htsjdk/variant/variantcontext/GenotypeUnitTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/variant/variantcontext/VariantContextUnitTest.java' -> `./src/test/java/htsjdk/variant/variantcontext/VariantContextUnitTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/variant/variantcontext/VariantJEXLContextUnitTest.java' -> `./src/test/java/htsjdk/variant/variantcontext/VariantJEXLContextUnitTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/variant/variantcontext/GenotypeLikelihoodsUnitTest.java' -> `./src/test/java/htsjdk/variant/variantcontext/GenotypeLikelihoodsUnitTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/variant/variantcontext/filter/HeterozygosityFilterTest.java' -> `./src/test/java/htsjdk/variant/variantcontext/filter/HeterozygosityFilterTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/variant/variantcontext/filter/PassingVariantFilterTest.java' -> `./src/test/java/htsjdk/variant/variantcontext/filter/PassingVariantFilterTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/variant/variantcontext/filter/AllPassFilter.java' -> `./src/test/java/htsjdk/variant/variantcontext/filter/AllPassFilter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/variant/variantcontext/filter/GenotypeQualityFilterTest.java' -> `./src/test/java/htsjdk/variant/variantcontext/filter/GenotypeQualityFilterTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/variant/variantcontext/filter/SnpFilterTest.java' -> `./src/test/java/htsjdk/variant/variantcontext/filter/SnpFilterTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/variant/variantcontext/filter/AllFailFilter.java' -> `./src/test/java/htsjdk/variant/variantcontext/filter/AllFailFilter.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/variant/variantcontext/filter/JavascriptVariantFilterTest.java' -> `./src/test/java/htsjdk/variant/variantcontext/filter/JavascriptVariantFilterTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/variant/variantcontext/filter/CompoundFilterTest.java' -> `./src/test/java/htsjdk/variant/variantcontext/filter/CompoundFilterTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/variant/variantcontext/filter/FilteringVariantContextIteratorTest.java' -> `./src/test/java/htsjdk/variant/variantcontext/filter/FilteringVariantContextIteratorTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/variant/variantcontext/writer/VariantContextWriterBuilderUnitTest.java' -> `./src/test/java/htsjdk/variant/variantcontext/writer/VariantContextWriterBuilderUnitTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/variant/variantcontext/writer/VariantContextWritersUnitTest.java' -> `./src/test/java/htsjdk/variant/variantcontext/writer/VariantContextWritersUnitTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/variant/variantcontext/writer/VCFWriterUnitTest.java' -> `./src/test/java/htsjdk/variant/variantcontext/writer/VCFWriterUnitTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/variant/variantcontext/writer/TabixOnTheFlyIndexCreationTest.java' -> `./src/test/java/htsjdk/variant/variantcontext/writer/TabixOnTheFlyIndexCreationTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/java/htsjdk/cram/io/ExternalCompressionTest.java' -> `./src/test/java/htsjdk/cram/io/ExternalCompressionTest.java'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/scala/htsjdk/UnitSpec.scala' -> `./src/test/scala/htsjdk/UnitSpec.scala'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/scala/htsjdk/samtools/util/StringUtilTest.scala' -> `./src/test/scala/htsjdk/samtools/util/StringUtilTest.scala'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/src/test/scala/htsjdk/samtools/fastq/FastqReaderWriterTest.scala' -> `./src/test/scala/htsjdk/samtools/fastq/FastqReaderWriterTest.scala'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/scripts/checkScalaAndJavaFiles.sh' -> `./scripts/checkScalaAndJavaFiles.sh'
`/gnu/store/1mcp9kdg7sfa9ls89jmr3ljddcady9km-java-htsjdk-2.10.1-checkout/scripts/explain_sam_flags.py' -> `./scripts/explain_sam_flags.py'
phase `unpack' succeeded after 0.4 seconds
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phase `remove-tests' succeeded after 0.0 seconds
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starting phase `patch-source-shebangs'
patch-shebang: ./gradlew: changing `/usr/bin/env bash' to `/gnu/store/2an4h5ndc22dv62q3l985ciq862q4bj7-bash-minimal-5.1.8/bin/bash'
patch-shebang: ./scripts/explain_sam_flags.py: warning: no binary for interpreter `python' found in $PATH
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starting phase `build'
Buildfile: /tmp/guix-build-java-htsjdk-2.10.1.drv-0/source/build.xml

compile:
    [mkdir] Created dir: /tmp/guix-build-java-htsjdk-2.10.1.drv-0/source/build/classes
    [javac] Compiling 572 source files to /tmp/guix-build-java-htsjdk-2.10.1.drv-0/source/build/classes
    [javac] Note: Some input files use or override a deprecated API.
    [javac] Note: Recompile with -Xlint:deprecation for details.
    [javac] Note: Some input files use unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.

manifest:
    [mkdir] Created dir: /tmp/guix-build-java-htsjdk-2.10.1.drv-0/source/build/manifest

jar:
    [mkdir] Created dir: /tmp/guix-build-java-htsjdk-2.10.1.drv-0/source/build/jar
      [jar] Building jar: /tmp/guix-build-java-htsjdk-2.10.1.drv-0/source/build/jar/htsjdk.jar

BUILD SUCCESSFUL
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phase `build' succeeded after 4.6 seconds
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Buildfile: /tmp/guix-build-java-htsjdk-2.10.1.drv-0/source/build.xml

install:
     [copy] Copying 1 file to /gnu/store/r7vlss68p0rpacam5q8mkq5n63kg6pbc-java-htsjdk-2.10.1/share/java

BUILD SUCCESSFUL
Total time: 0 seconds
phase `install' succeeded after 0.4 seconds
starting phase `reorder-jar-content'
repacking /gnu/store/r7vlss68p0rpacam5q8mkq5n63kg6pbc-java-htsjdk-2.10.1/share/java/htsjdk.jar
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  adding: htsjdk/tribble/exception/CodecLineParsingException.class (stored 0%)
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  adding: htsjdk/tribble/index/ (stored 0%)
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  adding: htsjdk/tribble/index/ChrIndex.class (stored 0%)
  adding: htsjdk/tribble/index/DynamicIndexCreator.class (stored 0%)
  adding: htsjdk/tribble/index/Index.class (stored 0%)
  adding: htsjdk/tribble/index/IndexCreator.class (stored 0%)
  adding: htsjdk/tribble/index/IndexFactory$1.class (stored 0%)
  adding: htsjdk/tribble/index/IndexFactory$FeatureIterator.class (stored 0%)
  adding: htsjdk/tribble/index/IndexFactory$IndexBalanceApproach.class (stored 0%)
  adding: htsjdk/tribble/index/IndexFactory$IndexType.class (stored 0%)
  adding: htsjdk/tribble/index/IndexFactory.class (stored 0%)
  adding: htsjdk/tribble/index/MutableIndex.class (stored 0%)
  adding: htsjdk/tribble/index/TribbleIndexCreator.class (stored 0%)
  adding: htsjdk/tribble/index/interval/ (stored 0%)
  adding: htsjdk/tribble/index/interval/Interval.class (stored 0%)
  adding: htsjdk/tribble/index/interval/IntervalIndexCreator.class (stored 0%)
  adding: htsjdk/tribble/index/interval/IntervalTree$Node.class (stored 0%)
  adding: htsjdk/tribble/index/interval/IntervalTree.class (stored 0%)
  adding: htsjdk/tribble/index/interval/IntervalTreeIndex$ChrIndex$1.class (stored 0%)
  adding: htsjdk/tribble/index/interval/IntervalTreeIndex$ChrIndex.class (stored 0%)
  adding: htsjdk/tribble/index/interval/IntervalTreeIndex.class (stored 0%)
  adding: htsjdk/tribble/index/interval/MutableInterval.class (stored 0%)
  adding: htsjdk/tribble/index/linear/ (stored 0%)
  adding: htsjdk/tribble/index/linear/LinearIndex$ChrIndex.class (stored 0%)
  adding: htsjdk/tribble/index/linear/LinearIndex.class (stored 0%)
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  adding: htsjdk/tribble/index/tabix/ (stored 0%)
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  adding: htsjdk/tribble/index/tabix/TabixIndexCreator$1.class (stored 0%)
  adding: htsjdk/tribble/index/tabix/TabixIndexCreator$TabixFeature.class (stored 0%)
  adding: htsjdk/tribble/index/tabix/TabixIndexCreator.class (stored 0%)
  adding: htsjdk/tribble/readers/ (stored 0%)
  adding: htsjdk/tribble/readers/AsciiLineReader.class (stored 0%)
  adding: htsjdk/tribble/readers/AsciiLineReaderIterator$TupleIterator.class (stored 0%)
  adding: htsjdk/tribble/readers/AsciiLineReaderIterator.class (stored 0%)
  adding: htsjdk/tribble/readers/LineIterator.class (stored 0%)
  adding: htsjdk/tribble/readers/LineIteratorImpl.class (stored 0%)
  adding: htsjdk/tribble/readers/LineReader.class (stored 0%)
  adding: htsjdk/tribble/readers/LongLineBufferedReader.class (stored 0%)
  adding: htsjdk/tribble/readers/Positional.class (stored 0%)
  adding: htsjdk/tribble/readers/PositionalBufferedStream.class (stored 0%)
  adding: htsjdk/tribble/readers/SynchronousLineReader.class (stored 0%)
  adding: htsjdk/tribble/readers/TabixIteratorLineReader.class (stored 0%)
  adding: htsjdk/tribble/readers/TabixReader$1.class (stored 0%)
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  adding: htsjdk/tribble/readers/TabixReader$IteratorImpl.class (stored 0%)
  adding: htsjdk/tribble/readers/TabixReader$TIndex.class (stored 0%)
  adding: htsjdk/tribble/readers/TabixReader$TIntv.class (stored 0%)
  adding: htsjdk/tribble/readers/TabixReader$TPair64.class (stored 0%)
  adding: htsjdk/tribble/readers/TabixReader.class (stored 0%)
  adding: htsjdk/tribble/util/ (stored 0%)
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  adding: htsjdk/tribble/util/LittleEndianInputStream.class (stored 0%)
  adding: htsjdk/tribble/util/LittleEndianOutputStream.class (stored 0%)
  adding: htsjdk/tribble/util/MathUtils$RunningStat.class (stored 0%)
  adding: htsjdk/tribble/util/MathUtils.class (stored 0%)
  adding: htsjdk/tribble/util/ParsingUtils.class (stored 0%)
  adding: htsjdk/tribble/util/RemoteURLHelper.class (stored 0%)
  adding: htsjdk/tribble/util/TabixUtils$TIndex.class (stored 0%)
  adding: htsjdk/tribble/util/TabixUtils$TIntv.class (stored 0%)
  adding: htsjdk/tribble/util/TabixUtils$TPair64.class (stored 0%)
  adding: htsjdk/tribble/util/TabixUtils.class (stored 0%)
  adding: htsjdk/tribble/util/URLHelper.class (stored 0%)
  adding: htsjdk/tribble/util/popgen/ (stored 0%)
  adding: htsjdk/tribble/util/popgen/HardyWeinbergCalculation.class (stored 0%)
  adding: htsjdk/variant/ (stored 0%)
  adding: htsjdk/variant/bcf2/ (stored 0%)
  adding: htsjdk/variant/bcf2/BCF2Codec$1.class (stored 0%)
  adding: htsjdk/variant/bcf2/BCF2Codec$LazyData.class (stored 0%)
  adding: htsjdk/variant/bcf2/BCF2Codec$SitesInfoForDecoding.class (stored 0%)
  adding: htsjdk/variant/bcf2/BCF2Codec.class (stored 0%)
  adding: htsjdk/variant/bcf2/BCF2Decoder$1.class (stored 0%)
  adding: htsjdk/variant/bcf2/BCF2Decoder.class (stored 0%)
  adding: htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders$1.class (stored 0%)
  adding: htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders$ADDecoder.class (stored 0%)
  adding: htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders$DPDecoder.class (stored 0%)
  adding: htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders$Decoder.class (stored 0%)
  adding: htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders$FTDecoder.class (stored 0%)
  adding: htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders$GQDecoder.class (stored 0%)
  adding: htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders$GTDecoder.class (stored 0%)
  adding: htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders$GenericDecoder.class (stored 0%)
  adding: htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders$PLDecoder.class (stored 0%)
  adding: htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders.class (stored 0%)
  adding: htsjdk/variant/bcf2/BCF2LazyGenotypesDecoder.class (stored 0%)
  adding: htsjdk/variant/bcf2/BCF2Type$1.class (stored 0%)
  adding: htsjdk/variant/bcf2/BCF2Type$2.class (stored 0%)
  adding: htsjdk/variant/bcf2/BCF2Type$3.class (stored 0%)
  adding: htsjdk/variant/bcf2/BCF2Type$4.class (stored 0%)
  adding: htsjdk/variant/bcf2/BCF2Type$5.class (stored 0%)
  adding: htsjdk/variant/bcf2/BCF2Type$6.class (stored 0%)
  adding: htsjdk/variant/bcf2/BCF2Type.class (stored 0%)
  adding: htsjdk/variant/bcf2/BCF2Utils$1.class (stored 0%)
  adding: htsjdk/variant/bcf2/BCF2Utils.class (stored 0%)
  adding: htsjdk/variant/bcf2/BCFVersion.class (stored 0%)
  adding: htsjdk/variant/example/ (stored 0%)
  adding: htsjdk/variant/example/PrintVariantsExample.class (stored 0%)
  adding: htsjdk/variant/utils/ (stored 0%)
  adding: htsjdk/variant/utils/GeneralUtils.class (stored 0%)
  adding: htsjdk/variant/utils/SAMSequenceDictionaryExtractor$1.class (stored 0%)
  adding: htsjdk/variant/utils/SAMSequenceDictionaryExtractor$TYPE$1.class (stored 0%)
  adding: htsjdk/variant/utils/SAMSequenceDictionaryExtractor$TYPE$2.class (stored 0%)
  adding: htsjdk/variant/utils/SAMSequenceDictionaryExtractor$TYPE$3.class (stored 0%)
  adding: htsjdk/variant/utils/SAMSequenceDictionaryExtractor$TYPE$4.class (stored 0%)
  adding: htsjdk/variant/utils/SAMSequenceDictionaryExtractor$TYPE$5.class (stored 0%)
  adding: htsjdk/variant/utils/SAMSequenceDictionaryExtractor$TYPE.class (stored 0%)
  adding: htsjdk/variant/utils/SAMSequenceDictionaryExtractor.class (stored 0%)
  adding: htsjdk/variant/variantcontext/ (stored 0%)
  adding: htsjdk/variant/variantcontext/Allele.class (stored 0%)
  adding: htsjdk/variant/variantcontext/CommonInfo.class (stored 0%)
  adding: htsjdk/variant/variantcontext/FastGenotype.class (stored 0%)
  adding: htsjdk/variant/variantcontext/Genotype.class (stored 0%)
  adding: htsjdk/variant/variantcontext/GenotypeBuilder.class (stored 0%)
  adding: htsjdk/variant/variantcontext/GenotypeJEXLContext$AttributeGetter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/GenotypeJEXLContext.class (stored 0%)
  adding: htsjdk/variant/variantcontext/GenotypeLikelihoods$GenotypeLikelihoodsAllelePair.class (stored 0%)
  adding: htsjdk/variant/variantcontext/GenotypeLikelihoods.class (stored 0%)
  adding: htsjdk/variant/variantcontext/GenotypeType.class (stored 0%)
  adding: htsjdk/variant/variantcontext/GenotypesContext$1.class (stored 0%)
  adding: htsjdk/variant/variantcontext/GenotypesContext$InOrderIterator.class (stored 0%)
  adding: htsjdk/variant/variantcontext/GenotypesContext.class (stored 0%)
  adding: htsjdk/variant/variantcontext/JEXLMap.class (stored 0%)
  adding: htsjdk/variant/variantcontext/JexlMissingValueTreatment.class (stored 0%)
  adding: htsjdk/variant/variantcontext/LazyGenotypesContext$LazyData.class (stored 0%)
  adding: htsjdk/variant/variantcontext/LazyGenotypesContext$LazyParser.class (stored 0%)
  adding: htsjdk/variant/variantcontext/LazyGenotypesContext.class (stored 0%)
  adding: htsjdk/variant/variantcontext/StructuralVariantType.class (stored 0%)
  adding: htsjdk/variant/variantcontext/VariantContext$1.class (stored 0%)
  adding: htsjdk/variant/variantcontext/VariantContext$Type.class (stored 0%)
  adding: htsjdk/variant/variantcontext/VariantContext$Validation.class (stored 0%)
  adding: htsjdk/variant/variantcontext/VariantContext.class (stored 0%)
  adding: htsjdk/variant/variantcontext/VariantContextBuilder.class (stored 0%)
  adding: htsjdk/variant/variantcontext/VariantContextComparator.class (stored 0%)
  adding: htsjdk/variant/variantcontext/VariantContextUtils$JexlVCMatchExp.class (stored 0%)
  adding: htsjdk/variant/variantcontext/VariantContextUtils.class (stored 0%)
  adding: htsjdk/variant/variantcontext/VariantJEXLContext$AttributeGetter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/VariantJEXLContext.class (stored 0%)
  adding: htsjdk/variant/variantcontext/filter/ (stored 0%)
  adding: htsjdk/variant/variantcontext/filter/CompoundFilter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/filter/FilteringIterator.class (stored 0%)
  adding: htsjdk/variant/variantcontext/filter/FilteringVariantContextIterator.class (stored 0%)
  adding: htsjdk/variant/variantcontext/filter/GenotypeQualityFilter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/filter/HeterozygosityFilter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/filter/JavascriptVariantFilter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/filter/PassingVariantFilter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/filter/SnpFilter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/filter/VariantContextFilter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/ (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/AsyncVariantContextWriter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/BCF2Encoder$1.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/BCF2Encoder.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/BCF2FieldEncoder$1.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/BCF2FieldEncoder$AtomicInt.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/BCF2FieldEncoder$Flag.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/BCF2FieldEncoder$Float.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/BCF2FieldEncoder$GenericInts.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/BCF2FieldEncoder$IntArray.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/BCF2FieldEncoder$StringOrCharacter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/BCF2FieldWriter$FTGenotypesWriter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/BCF2FieldWriter$GTWriter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/BCF2FieldWriter$GenericSiteWriter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/BCF2FieldWriter$GenotypesWriter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/BCF2FieldWriter$IGFGenotypesWriter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/BCF2FieldWriter$IntegerTypeGenotypesWriter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/BCF2FieldWriter$SiteWriter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/BCF2FieldWriter$StaticallyTypeGenotypesWriter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/BCF2FieldWriter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/BCF2FieldWriterManager$1.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/BCF2FieldWriterManager.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/BCF2Writer.class (stored 0%)
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  adding: htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors$1.class (stored 0%)
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  adding: htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors$AtomicAccessor.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors$DPAccessor.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors$GQAccessor.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors$PLAccessor.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/Options.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/SortingVariantContextWriter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/SortingVariantContextWriterBase$1.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/SortingVariantContextWriterBase$VCFRecord.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/SortingVariantContextWriterBase$VariantContextComparator.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/SortingVariantContextWriterBase.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/VCFWriter.class (stored 0%)
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  adding: htsjdk/variant/variantcontext/writer/VariantContextWriterBuilder$1.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/VariantContextWriterBuilder$OutputType.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/VariantContextWriterBuilder.class (stored 0%)
  adding: htsjdk/variant/vcf/ (stored 0%)
  adding: htsjdk/variant/vcf/AbstractVCFCodec$LazyVCFGenotypesParser.class (stored 0%)
  adding: htsjdk/variant/vcf/AbstractVCFCodec.class (stored 0%)
  adding: htsjdk/variant/vcf/VCF3Codec.class (stored 0%)
  adding: htsjdk/variant/vcf/VCF3Parser.class (stored 0%)
  adding: htsjdk/variant/vcf/VCF4Parser.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFCodec.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFCompoundHeaderLine$1.class (stored 0%)
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  adding: htsjdk/variant/vcf/VCFCompoundHeaderLine.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFConstants.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFContigHeaderLine$1.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFContigHeaderLine.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFEncoder.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFFileReader.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFFilterHeaderLine.class (stored 0%)
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  adding: htsjdk/variant/vcf/VCFHeader.class (stored 0%)
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  adding: htsjdk/variant/vcf/VCFHeaderLineCount.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFHeaderLineTranslator.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFHeaderLineType.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFHeaderVersion$1.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFHeaderVersion.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFIDHeaderLine.class (stored 0%)
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  adding: htsjdk/variant/vcf/VCFRecordCodec.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFSimpleHeaderLine.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFStandardHeaderLines$1.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFStandardHeaderLines$Standards.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFStandardHeaderLines.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFUtils$1.class (stored 0%)
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  adding: htsjdk/variant/vcf/VCFUtils.class (stored 0%)
phase `reorder-jar-content' succeeded after 0.2 seconds
starting phase `generate-jar-indices'
phase `generate-jar-indices' succeeded after 0.3 seconds
starting phase `strip-jar-timestamps'
repacking /gnu/store/r7vlss68p0rpacam5q8mkq5n63kg6pbc-java-htsjdk-2.10.1/share/java/htsjdk.jar
  adding: META-INF/ (stored 0%)
  adding: META-INF/INDEX.LIST (stored 0%)
  adding: META-INF/MANIFEST.MF (stored 0%)
  adding: htsjdk/ (stored 0%)
  adding: htsjdk/samtools/ (stored 0%)
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  adding: htsjdk/samtools/AbstractBAMFileIndex$MemoryMappedFileBuffer.class (stored 0%)
  adding: htsjdk/samtools/AbstractBAMFileIndex$RandomAccessFileBuffer.class (stored 0%)
  adding: htsjdk/samtools/AbstractBAMFileIndex.class (stored 0%)
  adding: htsjdk/samtools/AbstractSAMHeaderRecord.class (stored 0%)
  adding: htsjdk/samtools/AlignmentBlock.class (stored 0%)
  adding: htsjdk/samtools/AsyncSAMFileWriter.class (stored 0%)
  adding: htsjdk/samtools/BAMFileConstants.class (stored 0%)
  adding: htsjdk/samtools/BAMFileReader$1.class (stored 0%)
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  adding: htsjdk/samtools/BAMFileReader$BAMFileIndexUnmappedIterator.class (stored 0%)
  adding: htsjdk/samtools/BAMFileReader$BAMFileIterator.class (stored 0%)
  adding: htsjdk/samtools/BAMFileReader$BAMQueryFilteringIterator.class (stored 0%)
  adding: htsjdk/samtools/BAMFileReader$BAMStartingAtIteratorFilter.class (stored 0%)
  adding: htsjdk/samtools/BAMFileReader$EmptyBamIterator.class (stored 0%)
  adding: htsjdk/samtools/BAMFileReader.class (stored 0%)
  adding: htsjdk/samtools/BAMFileSpan.class (stored 0%)
  adding: htsjdk/samtools/BAMFileWriter.class (stored 0%)
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  adding: htsjdk/samtools/BAMIndexMetaData.class (stored 0%)
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  adding: htsjdk/samtools/BAMIndexer$BAMIndexBuilder.class (stored 0%)
  adding: htsjdk/samtools/BAMIndexer.class (stored 0%)
  adding: htsjdk/samtools/BAMIteratorFilter$FilteringIteratorState.class (stored 0%)
  adding: htsjdk/samtools/BAMIteratorFilter$IntervalComparison.class (stored 0%)
  adding: htsjdk/samtools/BAMIteratorFilter.class (stored 0%)
  adding: htsjdk/samtools/BAMQueryMultipleIntervalsIteratorFilter$1.class (stored 0%)
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  adding: htsjdk/samtools/BAMRecord.class (stored 0%)
  adding: htsjdk/samtools/BAMRecordCodec.class (stored 0%)
  adding: htsjdk/samtools/BamFileIoUtils.class (stored 0%)
  adding: htsjdk/samtools/BamIndexValidator$IndexValidationStringency.class (stored 0%)
  adding: htsjdk/samtools/BamIndexValidator.class (stored 0%)
  adding: htsjdk/samtools/Bin.class (stored 0%)
  adding: htsjdk/samtools/BinList$BinIterator.class (stored 0%)
  adding: htsjdk/samtools/BinList.class (stored 0%)
  adding: htsjdk/samtools/BinaryBAMIndexWriter.class (stored 0%)
  adding: htsjdk/samtools/BinaryCigarCodec.class (stored 0%)
  adding: htsjdk/samtools/BinaryTagCodec.class (stored 0%)
  adding: htsjdk/samtools/BinningIndexBuilder$FeatureToBeIndexed.class (stored 0%)
  adding: htsjdk/samtools/BinningIndexBuilder.class (stored 0%)
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  adding: htsjdk/samtools/util/SortingCollection$PeekFileRecordIteratorComparator.class (stored 0%)
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  adding: htsjdk/tribble/ (stored 0%)
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  adding: htsjdk/tribble/BinaryFeatureCodec.class (stored 0%)
  adding: htsjdk/tribble/CloseableTribbleIterator.class (stored 0%)
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  adding: htsjdk/tribble/FeatureReader.class (stored 0%)
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  adding: htsjdk/tribble/TribbleException$FeatureFileDoesntExist.class (stored 0%)
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  adding: htsjdk/tribble/bed/FullBEDFeature$Exon2.class (stored 0%)
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  adding: htsjdk/tribble/index/IndexCreator.class (stored 0%)
  adding: htsjdk/tribble/index/IndexFactory$1.class (stored 0%)
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  adding: htsjdk/tribble/index/MutableIndex.class (stored 0%)
  adding: htsjdk/tribble/index/TribbleIndexCreator.class (stored 0%)
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  adding: htsjdk/tribble/index/interval/IntervalIndexCreator.class (stored 0%)
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  adding: htsjdk/tribble/index/interval/IntervalTreeIndex$ChrIndex$1.class (stored 0%)
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  adding: htsjdk/tribble/readers/TabixReader$TIntv.class (stored 0%)
  adding: htsjdk/tribble/readers/TabixReader$TPair64.class (stored 0%)
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  adding: htsjdk/variant/bcf2/ (stored 0%)
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  adding: htsjdk/variant/bcf2/BCF2Codec$SitesInfoForDecoding.class (stored 0%)
  adding: htsjdk/variant/bcf2/BCF2Codec.class (stored 0%)
  adding: htsjdk/variant/bcf2/BCF2Decoder$1.class (stored 0%)
  adding: htsjdk/variant/bcf2/BCF2Decoder.class (stored 0%)
  adding: htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders$1.class (stored 0%)
  adding: htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders$ADDecoder.class (stored 0%)
  adding: htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders$DPDecoder.class (stored 0%)
  adding: htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders$Decoder.class (stored 0%)
  adding: htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders$FTDecoder.class (stored 0%)
  adding: htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders$GQDecoder.class (stored 0%)
  adding: htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders$GTDecoder.class (stored 0%)
  adding: htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders$GenericDecoder.class (stored 0%)
  adding: htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders$PLDecoder.class (stored 0%)
  adding: htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders.class (stored 0%)
  adding: htsjdk/variant/bcf2/BCF2LazyGenotypesDecoder.class (stored 0%)
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  adding: htsjdk/variant/bcf2/BCF2Type$6.class (stored 0%)
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  adding: htsjdk/variant/bcf2/BCF2Utils$1.class (stored 0%)
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  adding: htsjdk/variant/utils/SAMSequenceDictionaryExtractor$TYPE$2.class (stored 0%)
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  adding: htsjdk/variant/utils/SAMSequenceDictionaryExtractor$TYPE$4.class (stored 0%)
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  adding: htsjdk/variant/variantcontext/GenotypeJEXLContext$AttributeGetter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/GenotypeJEXLContext.class (stored 0%)
  adding: htsjdk/variant/variantcontext/GenotypeLikelihoods$GenotypeLikelihoodsAllelePair.class (stored 0%)
  adding: htsjdk/variant/variantcontext/GenotypeLikelihoods.class (stored 0%)
  adding: htsjdk/variant/variantcontext/GenotypeType.class (stored 0%)
  adding: htsjdk/variant/variantcontext/GenotypesContext$1.class (stored 0%)
  adding: htsjdk/variant/variantcontext/GenotypesContext$InOrderIterator.class (stored 0%)
  adding: htsjdk/variant/variantcontext/GenotypesContext.class (stored 0%)
  adding: htsjdk/variant/variantcontext/JEXLMap.class (stored 0%)
  adding: htsjdk/variant/variantcontext/JexlMissingValueTreatment.class (stored 0%)
  adding: htsjdk/variant/variantcontext/LazyGenotypesContext$LazyData.class (stored 0%)
  adding: htsjdk/variant/variantcontext/LazyGenotypesContext$LazyParser.class (stored 0%)
  adding: htsjdk/variant/variantcontext/LazyGenotypesContext.class (stored 0%)
  adding: htsjdk/variant/variantcontext/StructuralVariantType.class (stored 0%)
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  adding: htsjdk/variant/variantcontext/VariantContext$Validation.class (stored 0%)
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  adding: htsjdk/variant/variantcontext/VariantContextBuilder.class (stored 0%)
  adding: htsjdk/variant/variantcontext/VariantContextComparator.class (stored 0%)
  adding: htsjdk/variant/variantcontext/VariantContextUtils$JexlVCMatchExp.class (stored 0%)
  adding: htsjdk/variant/variantcontext/VariantContextUtils.class (stored 0%)
  adding: htsjdk/variant/variantcontext/VariantJEXLContext$AttributeGetter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/VariantJEXLContext.class (stored 0%)
  adding: htsjdk/variant/variantcontext/filter/ (stored 0%)
  adding: htsjdk/variant/variantcontext/filter/CompoundFilter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/filter/FilteringIterator.class (stored 0%)
  adding: htsjdk/variant/variantcontext/filter/FilteringVariantContextIterator.class (stored 0%)
  adding: htsjdk/variant/variantcontext/filter/GenotypeQualityFilter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/filter/HeterozygosityFilter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/filter/JavascriptVariantFilter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/filter/PassingVariantFilter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/filter/SnpFilter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/filter/VariantContextFilter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/ (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/AsyncVariantContextWriter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/BCF2Encoder$1.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/BCF2Encoder.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/BCF2FieldEncoder$1.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/BCF2FieldEncoder$AtomicInt.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/BCF2FieldEncoder$Flag.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/BCF2FieldEncoder$Float.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/BCF2FieldEncoder$GenericInts.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/BCF2FieldEncoder$IntArray.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/BCF2FieldEncoder$StringOrCharacter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/BCF2FieldWriter$FTGenotypesWriter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/BCF2FieldWriter$GTWriter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/BCF2FieldWriter$GenericSiteWriter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/BCF2FieldWriter$GenotypesWriter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/BCF2FieldWriter$IGFGenotypesWriter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/BCF2FieldWriter$IntegerTypeGenotypesWriter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/BCF2FieldWriter$SiteWriter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/BCF2FieldWriter$StaticallyTypeGenotypesWriter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/BCF2FieldWriter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/BCF2FieldWriterManager$1.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/BCF2FieldWriterManager.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/BCF2Writer.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/IndexingVariantContextWriter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors$1.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors$ADAccessor.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors$Accessor.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors$AtomicAccessor.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors$DPAccessor.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors$GQAccessor.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors$PLAccessor.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/Options.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/SortingVariantContextWriter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/SortingVariantContextWriterBase$1.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/SortingVariantContextWriterBase$VCFRecord.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/SortingVariantContextWriterBase$VariantContextComparator.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/SortingVariantContextWriterBase.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/VCFWriter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/VariantContextWriter.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/VariantContextWriterBuilder$1.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/VariantContextWriterBuilder$OutputType.class (stored 0%)
  adding: htsjdk/variant/variantcontext/writer/VariantContextWriterBuilder.class (stored 0%)
  adding: htsjdk/variant/vcf/ (stored 0%)
  adding: htsjdk/variant/vcf/AbstractVCFCodec$LazyVCFGenotypesParser.class (stored 0%)
  adding: htsjdk/variant/vcf/AbstractVCFCodec.class (stored 0%)
  adding: htsjdk/variant/vcf/VCF3Codec.class (stored 0%)
  adding: htsjdk/variant/vcf/VCF3Parser.class (stored 0%)
  adding: htsjdk/variant/vcf/VCF4Parser.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFCodec.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFCompoundHeaderLine$1.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFCompoundHeaderLine$SupportedHeaderLineType.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFCompoundHeaderLine.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFConstants.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFContigHeaderLine$1.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFContigHeaderLine.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFEncoder.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFFileReader.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFFilterHeaderLine.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFFormatHeaderLine.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFHeader$HEADER_FIELDS.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFHeader.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFHeaderLine.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFHeaderLineCount.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFHeaderLineTranslator.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFHeaderLineType.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFHeaderVersion$1.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFHeaderVersion.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFIDHeaderLine.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFInfoHeaderLine.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFLineParser.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFRecordCodec.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFSimpleHeaderLine.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFStandardHeaderLines$1.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFStandardHeaderLines$Standards.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFStandardHeaderLines.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFUtils$1.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFUtils$HeaderConflictWarner.class (stored 0%)
  adding: htsjdk/variant/vcf/VCFUtils.class (stored 0%)
phase `strip-jar-timestamps' succeeded after 0.2 seconds
starting phase `patch-shebangs'
phase `patch-shebangs' succeeded after 0.0 seconds
starting phase `strip'
phase `strip' succeeded after 0.0 seconds
starting phase `validate-runpath'
phase `validate-runpath' succeeded after 0.0 seconds
starting phase `validate-documentation-location'
phase `validate-documentation-location' succeeded after 0.0 seconds
starting phase `delete-info-dir-file'
phase `delete-info-dir-file' succeeded after 0.0 seconds
starting phase `patch-dot-desktop-files'
phase `patch-dot-desktop-files' succeeded after 0.0 seconds
starting phase `make-dynamic-linker-cache'
phase `make-dynamic-linker-cache' succeeded after 0.0 seconds
starting phase `install-license-files'
installing 0 license files from '.'
phase `install-license-files' succeeded after 0.0 seconds
starting phase `reset-gzip-timestamps'
phase `reset-gzip-timestamps' succeeded after 0.0 seconds
starting phase `compress-documentation'
phase `compress-documentation' succeeded after 0.0 seconds