data/beagle-5.1-200518+dfsg/bref/Bref3It.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/bref/Bref3Reader.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/bref/CompressBref3Writer.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/bref/AsIsBref3Writer.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/bref/BrefBlock.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/bref/UnBref3.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/bref/SeqCoder3.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/bref/BrefWriter.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/bref/Bref3.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/phase/FixedPhaseData.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/phase/RecombRegress.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/phase/PhaseBaum1.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/phase/EstPhase.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/phase/ImputeBaum.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/phase/HmmUpdater.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/phase/HapImputer.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/phase/SampleSeg.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/phase/FwdBwd.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/phase/PhaseIbs.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/phase/PhaseData.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/phase/CodedSteps.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/phase/Ibs2.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/phase/BestMatch.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/phase/PhaseStates.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/phase/LowFreqPhaseIbs.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/phase/PhaseLS.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/phase/PbwtPhaseIbs.java: Perl5 module source, UTF-8 Unicode text data/beagle-5.1-200518+dfsg/phase/AlleleImputer.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/gpl_license: ASCII text, with CRLF line terminators data/beagle-5.1-200518+dfsg/beagleutil/IntInterval.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/beagleutil/PbwtUpdater.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/beagleutil/ChromInterval.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/beagleutil/ThreadSafeIndexer.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/beagleutil/ChromIds.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/beagleutil/SampleIds.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/ints/IntList.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/ints/UnsignedByteArray.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/ints/IntIntMap.java: Perl5 module source, ASCII text, with CRLF, LF line terminators data/beagle-5.1-200518+dfsg/ints/IndexArray.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/ints/WrappedIntArray.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/ints/LongArray.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/ints/PackedIntArray.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/ints/CharArray.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/ints/IntArray.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/main/Par.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/main/CompHapSegment.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/main/Pedigree.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/main/RunStats.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/main/MainHelper.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/main/Main.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/main/WindowWriter.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/vcf/BasicGT.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/vcf/LowMafRefDiallelicGTRec.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/vcf/PositionMap.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/vcf/VcfIt.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/vcf/MarkerMap.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/vcf/Markers.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/vcf/GT.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/vcf/DuplicatesGTRec.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/vcf/GeneticMap.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/vcf/BitSetGTRec.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/vcf/VcfRecBuilder.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/vcf/TargetData.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/vcf/LowMafRefGTRec.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/vcf/VcfRecGTParser.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/vcf/VcfMetaInfo.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/vcf/HapsGT.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/vcf/GTRec.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/vcf/Marker.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/vcf/AllData.java: Perl5 module source, ASCII text, with CRLF, LF line terminators data/beagle-5.1-200518+dfsg/vcf/IntervalVcfIt.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/vcf/Data.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/vcf/RefIt.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/vcf/MarkerIndices.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/vcf/RestrictedVcfWindow.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/vcf/VcfHeader.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/vcf/SeqCodedRefGTRec.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/vcf/Window.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/vcf/RestrictedGT.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/vcf/RefGT.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/vcf/RefGTRec.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/vcf/PlinkGenMap.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/vcf/VcfWriter.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/vcf/MarkerContainer.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/vcf/Samples.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/vcf/WindowIt.java: Perl5 module source, ASCII text, with CRLF, LF line terminators data/beagle-5.1-200518+dfsg/vcf/VcfRec.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/vcf/BasicMarker.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/vcf/FilterUtil.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/vcf/SplicedGT.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/imp/ImpLSBaum.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/imp/StateProbs.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/imp/StateProbsFactory.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/imp/ImputedRecBuilder.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/imp/RefHapHash.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/imp/ImpStates.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/imp/CodedSteps.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/imp/ImpIbs.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/imp/ImpLS.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/imp/HaplotypeCoder.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/imp/ImpData.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/imp/ImputedVcfWriter.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/math/Regress.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/blbutil/FloatList.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/blbutil/Validate.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/blbutil/FloatArray.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/blbutil/BGZIPOutputStream.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/blbutil/StringUtil.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/blbutil/Pair.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/blbutil/Filter.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/blbutil/FileUtil.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/blbutil/FileIt.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/blbutil/Const.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/blbutil/DoubleArray.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/blbutil/MultiThreadUtils.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/blbutil/Utilities.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/blbutil/SampleFileIt.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/blbutil/InputIt.java: Perl5 module source, ASCII text data/beagle-5.1-200518+dfsg/debian/README.source: UTF-8 Unicode text data/beagle-5.1-200518+dfsg/debian/beagle-doc.doc-base: ASCII text data/beagle-5.1-200518+dfsg/debian/beagle-doc.install: ASCII text data/beagle-5.1-200518+dfsg/debian/beagle-doc.lintian-overrides: ASCII text data/beagle-5.1-200518+dfsg/debian/beagle.1: troff or preprocessor input, UTF-8 Unicode text data/beagle-5.1-200518+dfsg/debian/beagle.install: ASCII text data/beagle-5.1-200518+dfsg/debian/beagle.manpages: ASCII text data/beagle-5.1-200518+dfsg/debian/bref3.1: troff or preprocessor input, UTF-8 Unicode text data/beagle-5.1-200518+dfsg/debian/changelog: UTF-8 Unicode text data/beagle-5.1-200518+dfsg/debian/clean: ASCII text data/beagle-5.1-200518+dfsg/debian/control: UTF-8 Unicode text data/beagle-5.1-200518+dfsg/debian/copyright: UTF-8 Unicode text data/beagle-5.1-200518+dfsg/debian/local/bin/beagle: POSIX shell script, ASCII text executable data/beagle-5.1-200518+dfsg/debian/local/bin/bref3: POSIX shell script, ASCII text executable data/beagle-5.1-200518+dfsg/debian/patches/01_Update_htsjtk.patch: unified diff output, UTF-8 Unicode text data/beagle-5.1-200518+dfsg/debian/patches/series: ASCII text data/beagle-5.1-200518+dfsg/debian/rules: a /usr/bin/make -f script, ASCII text executable data/beagle-5.1-200518+dfsg/debian/salsa-ci.yml: ASCII text data/beagle-5.1-200518+dfsg/debian/source/format: ASCII text data/beagle-5.1-200518+dfsg/debian/source/include-binaries: ASCII text data/beagle-5.1-200518+dfsg/debian/tests/control: ASCII text data/beagle-5.1-200518+dfsg/debian/tests/run-sample-analysis: POSIX shell script, UTF-8 Unicode text executable data/beagle-5.1-200518+dfsg/debian/upstream/metadata: ASCII text data/beagle-5.1-200518+dfsg/debian/upstream.docs/README: ISO-8859 text data/beagle-5.1-200518+dfsg/debian/upstream.docs/beagle_4.1_09Feb16.docx: Microsoft Word 2007+ data/beagle-5.1-200518+dfsg/debian/upstream.docs/beagle_5.1.pdf: PDF document, version 1.5 (password protected) data/beagle-5.1-200518+dfsg/debian/upstream.docs/release_notes: ASCII text data/beagle-5.1-200518+dfsg/debian/upstream.docs/release_notes_4.1: ASCII text, with CRLF line terminators data/beagle-5.1-200518+dfsg/debian/upstream.docs/run.beagle.example: Bourne-Again shell script, ASCII text executable data/beagle-5.1-200518+dfsg/debian/upstream.docs/test.vcf: Variant Call Format (VCF) version 4.1, ASCII text, with very long lines data/beagle-5.1-200518+dfsg/debian/watch: ASCII text data/beagle-5.1-200518+dfsg/.pc/.version: ASCII text data/beagle-5.1-200518+dfsg/.pc/.quilt_patches: ASCII text data/beagle-5.1-200518+dfsg/.pc/.quilt_series: ASCII text data/beagle-5.1-200518+dfsg/.pc/applied-patches: ASCII text data/beagle-5.1-200518+dfsg/.pc/01_Update_htsjtk.patch/blbutil/InputIt.java: Perl5 module source, ASCII text