[med-svn] [htsjdk] branch debian/jessie-backports updated (b768075 -> a12dc99)
Andreas Tille
tille at debian.org
Sun Jun 25 08:13:45 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch debian/jessie-backports
in repository htsjdk.
from b768075 Fix JAVA_HOME
adds 7170221 Take over change from debian/jessie-backports branch to successfully obtain JAVA_HOME
adds 759cd02 Imported Upstream version 2.3.0+dfsg.1
adds 781d11d Merge tag 'upstream/2.3.0+dfsg.1'
adds 4e7593d New upstream version
adds cf41a49 Refresh patches
adds 640fd54 Bump Standards-Version to 3.9.8
adds a456695 Skip tests checking the use of the local zip implementation
adds c9883b4 Imported Upstream version 2.5.0
adds 23d85cb Merge tag 'upstream/2.5.0'
adds 17e0b6f Simplified watch file, new upstream version
adds 5fdb340 Imported Upstream version 2.5.0+dfsg
adds 843f684 Merge tag 'upstream/2.5.0+dfsg'
adds 5e2962b Build system changed to gradle - patch does not apply any more
adds a10cf9a Addapt patches
adds f102f23 Try to adapt gradle build system by removing plugins we can not download
adds e143bf7 Try to rework the patch for gradle (but failed :-()
adds 2606dd7 Upstream has changed build system to gradle
adds 1589747 gradle-wrapper is a convenient library already packaged
adds b1b51fd Set version from debian/changelog
adds 95f0e17 Update build system to gradle
adds 876cb43 Fix install path with the new build system
adds f89051a Fix version handling
adds ceef19d No other convenient libraries are provided in lib/
adds 3a308e0 Re-enable tests and doc
adds cb3c600 fix copyright
adds ce6857a remove dfsg suffix in version
adds 9f7ee36 no need to build sources and javadoc jars
adds 188637e Add a changelog line about gradle build system
adds d3e2779 temporary disabling tests
adds 023be94 Imported Upstream version 2.5.0+dfsg.2
adds 434afc6 Merge tag 'upstream/2.5.0+dfsg.2' into sid
adds b205f83 Rewrote copyright and remove convenience jar file for gradle
adds ec109d5 Correctly handle dfsg version suffix
adds 098b45c cleanup changelog
adds 1dfc23d Add a maven2 pom file for htsjdk
adds ac92dd2 Force the dependency on libngs-java to be sure the pom file is installed
adds 4de4cd3 Revert "temporary disabling tests"
adds eba587e Add missing build dependency
adds 7db3ee6 Ready for upload
adds 8293063 Cleanup classpath and dependencies
adds 58abd89 Tweak build-dependencies and classpath
adds 72a19cc Remove some more tests needing http or ftp connections
adds 48d1ae3 Exclude more tests
adds 2fd37cd Remove last test that requires online connection
adds 262dc02 Upload to unstable
adds 00ff79c New upstream version 2.6.1+dfsg
adds d86706f Merge tag 'upstream/2.6.1+dfsg'
adds 191617e new upstream version
adds b3ba8c0 Allow suffix for dfsg when repackaging
adds 1c8643b New upstream version 2.7.0+dfsg
adds a877967 Merge tag 'upstream/2.7.0+dfsg' into sid
adds fc51e02 New upstream version
adds 7b394d9 Update copyright file
adds 97034e3 Upload to unstable
adds fda2dfd Re-add the missing entry in changelog
adds 2ea9ded Re-add file SAMFileReader.java featuring an outdated API which is used by Artemis and FastQC
adds 022e46c Revert latest change since upstream has intentionally removed an old API (https://github.com/samtools/htsjdk/issues/767)
adds ed6db4b New upstream version 2.8.1+dfsg
adds b306827 Merge tag 'upstream/2.8.1+dfsg'
adds 6b9cdb2 New upstream version
adds 185773c debhelper 10
adds 9bea108 d/watch: version=4
adds 50741e4 Add missing depends on junit4
adds ef89533 Update changelog
new 4da2cde Merge tag 'debian/2.8.1+dfsg-1' into debian/jessie-backports
new c502557 Rebuild for jessie-backports
new a12dc99 TODO: backporting gradle 3.2.1 which is quite some effort
The 3 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.classpath | 10 -
.github/PULL_REQUEST_TEMPLATE.md | 2 +
.gitignore | 25 +-
.idea/.name | 1 -
.idea/compiler.xml | 23 -
.idea/copyright/profiles_settings.xml | 3 -
.idea/encodings.xml | 4 -
.idea/modules.xml | 9 -
.idea/modules/htsjdk-build.iml | 81 -
.idea/modules/htsjdk.iml | 44 -
.idea/sbt.xml | 22 -
.idea/scala_compiler.xml | 6 -
.idea/scopes/scope_settings.xml | 5 -
.idea/vcs.xml | 7 -
.project | 17 -
.travis.yml | 23 +-
README.md | 73 +
build.gradle | 227 +
build.sbt | 147 -
build.xml | 269 +-
debian/broadinstitute-keyring.gpg | Bin 0 -> 1220 bytes
debian/changelog | 67 +
debian/compat | 2 +-
debian/control | 22 +-
debian/copyright | 579 ++-
debian/htsjdk.pom | 73 +
debian/htsjdk.pom.asc | 11 +
debian/libhtsjdk-java-doc.javadoc | 2 +-
debian/libhtsjdk-java.classpath | 2 +-
debian/libhtsjdk-java.install | 2 +-
debian/libhtsjdk-java.jlibs | 2 +-
debian/libhtsjdk-java.poms | 29 +
debian/maven.rules | 19 +
debian/patches/10-build.xml | 67 -
debian/patches/10-build.xml.patch | 18 +
debian/patches/11-snappy-java-compatibility.patch | 4 +-
debian/patches/12-use_libjbzip2-java | 27 -
debian/patches/13-skip_network_tests | 843 +++-
debian/patches/20-fix-version.patch | 65 +
debian/patches/50-fix-build.patch | 11 +
debian/patches/series | 5 +-
debian/rules | 33 +-
debian/source/include-binaries | 1 +
debian/watch | 4 +-
etc/test/junit-noframes.xsl | 581 ---
etc/test/testng.css | 26 -
gradle/wrapper/gradle-wrapper.properties | 6 +
gradlew | 164 +
htsjdk.iml | 66 -
htsjdk.ipr | 352 --
project/plugins.sbt | 5 -
{src/scripts => scripts}/explain_sam_flags.py | 0
{src/scripts => scripts}/release_picard.sh | 0
src/c/inteldeflater/IntelDeflater.c | 247 -
src/java/htsjdk/samtools/AbstractBAMFileIndex.java | 720 ---
.../htsjdk/samtools/AbstractSAMHeaderRecord.java | 115 -
src/java/htsjdk/samtools/BAMFileReader.java | 968 ----
src/java/htsjdk/samtools/BAMFileWriter.java | 193 -
src/java/htsjdk/samtools/BAMIndexMetaData.java | 271 --
src/java/htsjdk/samtools/BAMIndexer.java | 295 --
src/java/htsjdk/samtools/BinningIndexBuilder.java | 187 -
.../htsjdk/samtools/CRAMContainerStreamWriter.java | 496 --
src/java/htsjdk/samtools/CRAMFileReader.java | 625 ---
src/java/htsjdk/samtools/CRAMFileWriter.java | 167 -
src/java/htsjdk/samtools/CRAMIndexer.java | 474 --
src/java/htsjdk/samtools/CRAMIterator.java | 307 --
.../htsjdk/samtools/DefaultSAMRecordFactory.java | 54 -
src/java/htsjdk/samtools/Defaults.java | 111 -
.../htsjdk/samtools/DuplicateScoringStrategy.java | 130 -
src/java/htsjdk/samtools/DuplicateSetIterator.java | 153 -
src/java/htsjdk/samtools/GenomicIndexUtil.java | 100 -
.../htsjdk/samtools/MergingSamRecordIterator.java | 237 -
.../SAMBinaryTagAndUnsignedArrayValue.java | 60 -
src/java/htsjdk/samtools/SAMBinaryTagAndValue.java | 175 -
src/java/htsjdk/samtools/SAMFileHeader.java | 393 --
src/java/htsjdk/samtools/SAMFileReader.java | 798 ----
.../htsjdk/samtools/SAMFileTruncatedReader.java | 69 -
src/java/htsjdk/samtools/SAMFileWriterFactory.java | 464 --
src/java/htsjdk/samtools/SAMFlag.java | 110 -
src/java/htsjdk/samtools/SAMLineParser.java | 469 --
src/java/htsjdk/samtools/SAMRecord.java | 2284 ---------
src/java/htsjdk/samtools/SAMRecordSetBuilder.java | 577 ---
src/java/htsjdk/samtools/SAMRecordUtil.java | 81 -
.../htsjdk/samtools/SAMSequenceDictionary.java | 270 --
src/java/htsjdk/samtools/SAMSequenceRecord.java | 247 -
src/java/htsjdk/samtools/SAMTextHeaderCodec.java | 468 --
src/java/htsjdk/samtools/SAMTextWriter.java | 188 -
src/java/htsjdk/samtools/SAMUtils.java | 1099 -----
src/java/htsjdk/samtools/SRAFileReader.java | 306 --
src/java/htsjdk/samtools/SRAIterator.java | 248 -
src/java/htsjdk/samtools/SamFileHeaderMerger.java | 780 ---
src/java/htsjdk/samtools/SamFileValidator.java | 856 ----
src/java/htsjdk/samtools/SamFiles.java | 81 -
src/java/htsjdk/samtools/SamInputResource.java | 360 --
src/java/htsjdk/samtools/SamPairUtil.java | 480 --
src/java/htsjdk/samtools/SamReader.java | 597 ---
src/java/htsjdk/samtools/SamReaderFactory.java | 492 --
src/java/htsjdk/samtools/SamStreams.java | 93 -
src/java/htsjdk/samtools/TextTagCodec.java | 330 --
src/java/htsjdk/samtools/cram/CRAIEntry.java | 148 -
src/java/htsjdk/samtools/cram/CRAIIndex.java | 164 -
.../htsjdk/samtools/cram/build/CramNormalizer.java | 347 --
src/java/htsjdk/samtools/cram/build/Utils.java | 52 -
.../htsjdk/samtools/cram/common/CramVersions.java | 11 -
.../cram/encoding/reader/DataReaderFactory.java | 230 -
.../samtools/cram/io/ExternalCompression.java | 151 -
.../htsjdk/samtools/cram/ref/ReferenceSource.java | 265 --
.../samtools/cram/structure/CompressionHeader.java | 299 --
.../samtools/cram/structure/ContainerHeaderIO.java | 88 -
src/java/htsjdk/samtools/cram/structure/Slice.java | 255 -
.../htsjdk/samtools/fastq/FastqWriterFactory.java | 31 -
.../htsjdk/samtools/filter/FilteringIterator.java | 154 -
.../htsjdk/samtools/filter/IntervalFilter.java | 99 -
src/java/htsjdk/samtools/liftover/LiftOver.java | 292 --
src/java/htsjdk/samtools/metrics/MetricsFile.java | 592 ---
.../samtools/reference/ReferenceSequence.java | 72 -
.../seekablestream/ByteArraySeekableStream.java | 75 -
.../seekablestream/SeekableMemoryStream.java | 64 -
.../seekablestream/SeekableStreamFactory.java | 95 -
src/java/htsjdk/samtools/sra/ReferenceCache.java | 79 -
src/java/htsjdk/samtools/sra/SRAAccession.java | 136 -
.../htsjdk/samtools/sra/SRAAlignmentIterator.java | 194 -
.../samtools/sra/SRAIndexedSequenceFile.java | 121 -
.../htsjdk/samtools/util/AbstractAsyncWriter.java | 121 -
.../samtools/util/BlockCompressedInputStream.java | 512 --
.../samtools/util/BlockCompressedOutputStream.java | 336 --
src/java/htsjdk/samtools/util/BlockGunzipper.java | 115 -
.../htsjdk/samtools/util/CloseableIterator.java | 45 -
src/java/htsjdk/samtools/util/CollectionUtil.java | 185 -
src/java/htsjdk/samtools/util/Histogram.java | 480 --
src/java/htsjdk/samtools/util/IOUtil.java | 965 ----
src/java/htsjdk/samtools/util/IntervalList.java | 772 ---
src/java/htsjdk/samtools/util/Lazy.java | 39 -
src/java/htsjdk/samtools/util/Log.java | 214 -
src/java/htsjdk/samtools/util/Objects.java | 12 -
src/java/htsjdk/samtools/util/OverlapDetector.java | 126 -
.../samtools/util/QualityEncodingDetector.java | 405 --
.../htsjdk/samtools/util/SamLocusIterator.java | 552 ---
.../util/SamRecordIntervalIteratorFactory.java | 157 -
src/java/htsjdk/samtools/util/SequenceUtil.java | 1092 -----
.../htsjdk/samtools/util/SortingCollection.java | 532 ---
src/java/htsjdk/samtools/util/StringUtil.java | 548 ---
src/java/htsjdk/samtools/util/TestUtil.java | 92 -
src/java/htsjdk/samtools/util/Tuple.java | 42 -
.../htsjdk/samtools/util/zip/DeflaterFactory.java | 78 -
.../htsjdk/samtools/util/zip/IntelDeflater.java | 567 ---
src/java/htsjdk/samtools/util/zip/ZStreamRef.java | 48 -
src/java/htsjdk/tribble/AbstractFeatureReader.java | 183 -
src/java/htsjdk/tribble/AsciiFeatureCodec.java | 97 -
src/java/htsjdk/tribble/BinaryFeatureCodec.java | 43 -
src/java/htsjdk/tribble/Feature.java | 41 -
src/java/htsjdk/tribble/FeatureCodec.java | 122 -
src/java/htsjdk/tribble/SimpleFeature.java | 58 -
src/java/htsjdk/tribble/TabixFeatureReader.java | 221 -
.../tribble/TribbleIndexedFeatureReader.java | 545 ---
src/java/htsjdk/tribble/bed/BEDCodec.java | 227 -
src/java/htsjdk/tribble/bed/SimpleBEDFeature.java | 148 -
src/java/htsjdk/tribble/example/CountRecords.java | 204 -
.../htsjdk/tribble/example/ExampleBinaryCodec.java | 128 -
.../htsjdk/tribble/gelitext/GeliTextFeature.java | 154 -
src/java/htsjdk/tribble/index/AbstractIndex.java | 448 --
src/java/htsjdk/tribble/index/Index.java | 91 -
src/java/htsjdk/tribble/index/IndexCreator.java | 50 -
src/java/htsjdk/tribble/index/IndexFactory.java | 509 --
.../htsjdk/tribble/index/TribbleIndexCreator.java | 37 -
.../index/interval/IntervalIndexCreator.java | 159 -
.../tribble/index/linear/LinearIndexCreator.java | 126 -
.../htsjdk/tribble/index/tabix/TabixIndex.java | 369 --
.../tribble/index/tabix/TabixIndexCreator.java | 202 -
.../tribble/readers/AsynchronousLineReader.java | 98 -
.../htsjdk/tribble/readers/LineReaderUtil.java | 94 -
src/java/htsjdk/variant/bcf2/BCF2Codec.java | 494 --
.../htsjdk/variant/variantcontext/CommonInfo.java | 295 --
.../variant/variantcontext/FastGenotype.java | 170 -
.../htsjdk/variant/variantcontext/Genotype.java | 666 ---
.../variant/variantcontext/GenotypeBuilder.java | 394 --
.../htsjdk/variant/variantcontext/JEXLMap.java | 238 -
.../variant/variantcontext/VariantContext.java | 1735 -------
.../variantcontext/VariantContextBuilder.java | 500 --
.../variantcontext/VariantContextComparator.java | 105 -
.../variantcontext/VariantContextUtils.java | 450 --
.../variant/variantcontext/VariantJEXLContext.java | 104 -
.../variantcontext/filter/FilteringIterator.java | 127 -
.../variantcontext/writer/BCF2FieldWriter.java | 323 --
.../variant/variantcontext/writer/BCF2Writer.java | 443 --
.../writer/IndexingVariantContextWriter.java | 230 -
.../writer/SortingVariantContextWriterBase.java | 201 -
.../writer/VariantContextWriterBuilder.java | 505 --
.../writer/VariantContextWriterFactory.java | 282 --
src/java/htsjdk/variant/vcf/AbstractVCFCodec.java | 786 ---
src/java/htsjdk/variant/vcf/VCFConstants.java | 127 -
src/java/htsjdk/variant/vcf/VCFEncoder.java | 382 --
src/java/htsjdk/variant/vcf/VCFFileReader.java | 153 -
.../htsjdk/variant/vcf/VCFFilterHeaderLine.java | 69 -
.../variant/vcf/VCFHeaderLineTranslator.java | 157 -
.../htsjdk/variant/vcf/VCFStandardHeaderLines.java | 256 -
.../java/htsjdk/samtools/AbstractBAMFileIndex.java | 721 +++
.../htsjdk/samtools/AbstractSAMHeaderRecord.java | 116 +
.../java/htsjdk/samtools/AlignmentBlock.java | 0
.../java/htsjdk/samtools/AsyncSAMFileWriter.java | 0
.../java/htsjdk/samtools/BAMFileConstants.java | 0
src/main/java/htsjdk/samtools/BAMFileReader.java | 913 ++++
.../java/htsjdk/samtools/BAMFileSpan.java | 0
src/main/java/htsjdk/samtools/BAMFileWriter.java | 200 +
src/{ => main}/java/htsjdk/samtools/BAMIndex.java | 0
.../java/htsjdk/samtools/BAMIndexContent.java | 0
.../java/htsjdk/samtools/BAMIndexMetaData.java | 271 ++
.../java/htsjdk/samtools/BAMIndexWriter.java | 0
src/main/java/htsjdk/samtools/BAMIndexer.java | 313 ++
.../java/htsjdk/samtools/BAMIteratorFilter.java | 26 +
.../BAMQueryMultipleIntervalsIteratorFilter.java | 59 +
src/{ => main}/java/htsjdk/samtools/BAMRecord.java | 0
.../java/htsjdk/samtools/BAMRecordCodec.java | 0
.../java/htsjdk/samtools/BamFileIoUtils.java | 0
.../java/htsjdk/samtools/BamIndexValidator.java | 0
src/{ => main}/java/htsjdk/samtools/Bin.java | 0
src/{ => main}/java/htsjdk/samtools/BinList.java | 0
.../java/htsjdk/samtools/BinaryBAMIndexWriter.java | 0
.../java/htsjdk/samtools/BinaryCigarCodec.java | 0
.../java/htsjdk/samtools/BinaryTagCodec.java | 0
.../java/htsjdk/samtools/BinningIndexBuilder.java | 187 +
.../java/htsjdk/samtools/BinningIndexContent.java | 0
.../java/htsjdk/samtools/BrowseableBAMIndex.java | 0
src/main/java/htsjdk/samtools/CRAMBAIIndexer.java | 474 ++
src/main/java/htsjdk/samtools/CRAMCRAIIndexer.java | 135 +
.../htsjdk/samtools/CRAMContainerStreamWriter.java | 495 ++
src/main/java/htsjdk/samtools/CRAMFileReader.java | 559 +++
src/main/java/htsjdk/samtools/CRAMFileWriter.java | 168 +
src/main/java/htsjdk/samtools/CRAMIterator.java | 310 ++
.../java/htsjdk/samtools/CachingBAMFileIndex.java | 0
.../samtools/ChainedDownsamplingIterator.java | 0
src/{ => main}/java/htsjdk/samtools/Chunk.java | 0
src/{ => main}/java/htsjdk/samtools/Cigar.java | 0
.../java/htsjdk/samtools/CigarElement.java | 0
.../java/htsjdk/samtools/CigarOperator.java | 0
.../samtools/ComparableSamRecordIterator.java | 0
.../ConstantMemoryDownsamplingIterator.java | 0
.../samtools/CoordinateSortedPairInfoMap.java | 0
.../java/htsjdk/samtools/CustomReaderFactory.java | 0
.../htsjdk/samtools/DefaultSAMRecordFactory.java | 54 +
src/main/java/htsjdk/samtools/Defaults.java | 174 +
.../htsjdk/samtools/DiskBasedBAMFileIndex.java | 0
.../java/htsjdk/samtools/DownsamplingIterator.java | 0
.../samtools/DownsamplingIteratorFactory.java | 0
.../htsjdk/samtools/DuplicateScoringStrategy.java | 138 +
.../java/htsjdk/samtools/DuplicateSet.java | 0
.../java/htsjdk/samtools/DuplicateSetIterator.java | 172 +
.../htsjdk/samtools/FileTruncatedException.java | 0
.../java/htsjdk/samtools/FixBAMFile.java | 0
.../java/htsjdk/samtools/GenomicIndexUtil.java | 100 +
.../samtools/HighAccuracyDownsamplingIterator.java | 0
.../java/htsjdk/samtools/LinearIndex.java | 0
.../htsjdk/samtools/MergingSamRecordIterator.java | 238 +
.../samtools/NotPrimarySkippingIterator.java | 0
.../java/htsjdk/samtools/QueryInterval.java | 0
.../java/htsjdk/samtools/ReservedTagConstants.java | 0
.../SAMBinaryTagAndUnsignedArrayValue.java | 65 +
.../java/htsjdk/samtools/SAMBinaryTagAndValue.java | 251 +
.../java/htsjdk/samtools/SAMException.java | 0
src/main/java/htsjdk/samtools/SAMFileHeader.java | 399 ++
.../java/htsjdk/samtools/SAMFileSource.java | 0
.../java/htsjdk/samtools/SAMFileSpan.java | 0
.../java/htsjdk/samtools/SAMFileWriter.java | 0
.../java/htsjdk/samtools/SAMFileWriterFactory.java | 505 ++
.../java/htsjdk/samtools/SAMFileWriterImpl.java | 0
src/main/java/htsjdk/samtools/SAMFlag.java | 110 +
.../java/htsjdk/samtools/SAMFormatException.java | 0
.../htsjdk/samtools/SAMHeaderRecordComparator.java | 0
src/main/java/htsjdk/samtools/SAMLineParser.java | 487 ++
.../java/htsjdk/samtools/SAMProgramRecord.java | 0
.../java/htsjdk/samtools/SAMReadGroupRecord.java | 0
src/main/java/htsjdk/samtools/SAMRecord.java | 2378 ++++++++++
.../java/htsjdk/samtools/SAMRecordComparator.java | 0
.../samtools/SAMRecordCoordinateComparator.java | 0
.../samtools/SAMRecordDuplicateComparator.java | 0
.../java/htsjdk/samtools/SAMRecordFactory.java | 0
.../java/htsjdk/samtools/SAMRecordIterator.java | 0
.../samtools/SAMRecordQueryHashComparator.java | 0
.../samtools/SAMRecordQueryNameComparator.java | 0
.../java/htsjdk/samtools/SAMRecordSetBuilder.java | 576 +++
src/main/java/htsjdk/samtools/SAMRecordUtil.java | 77 +
.../htsjdk/samtools/SAMSequenceDictionary.java | 355 ++
.../samtools/SAMSequenceDictionaryCodec.java | 114 +
.../java/htsjdk/samtools/SAMSequenceRecord.java | 248 +
.../java/htsjdk/samtools/SAMSortOrderChecker.java | 0
src/{ => main}/java/htsjdk/samtools/SAMTag.java | 0
.../java/htsjdk/samtools/SAMTagUtil.java | 0
.../java/htsjdk/samtools/SAMTestUtil.java | 0
.../java/htsjdk/samtools/SAMTextHeaderCodec.java | 500 ++
.../java/htsjdk/samtools/SAMTextReader.java | 0
src/main/java/htsjdk/samtools/SAMTextWriter.java | 221 +
src/{ => main}/java/htsjdk/samtools/SAMTools.java | 0
src/main/java/htsjdk/samtools/SAMUtils.java | 1226 +++++
.../java/htsjdk/samtools/SAMValidationError.java | 0
src/{ => main}/java/htsjdk/samtools/SQTagUtil.java | 0
src/main/java/htsjdk/samtools/SRAFileReader.java | 309 ++
src/{ => main}/java/htsjdk/samtools/SRAIndex.java | 0
src/main/java/htsjdk/samtools/SRAIterator.java | 256 +
.../java/htsjdk/samtools/SamFileHeaderMerger.java | 786 +++
.../java/htsjdk/samtools/SamFileValidator.java | 872 ++++
src/main/java/htsjdk/samtools/SamFiles.java | 98 +
src/main/java/htsjdk/samtools/SamFlagField.java | 203 +
.../java/htsjdk/samtools/SamIndexes.java | 0
.../java/htsjdk/samtools/SamInputResource.java | 497 ++
src/main/java/htsjdk/samtools/SamPairUtil.java | 510 ++
src/main/java/htsjdk/samtools/SamReader.java | 621 +++
.../java/htsjdk/samtools/SamReaderFactory.java | 568 +++
src/main/java/htsjdk/samtools/SamStreams.java | 164 +
.../SecondaryOrSupplementarySkippingIterator.java | 0
.../StreamInflatingIndexingOutputStream.java | 0
.../samtools/TagValueAndUnsignedArrayFlag.java | 0
.../java/htsjdk/samtools/TextCigarCodec.java | 0
src/main/java/htsjdk/samtools/TextTagCodec.java | 331 ++
.../htsjdk/samtools/TextualBAMIndexWriter.java | 0
.../java/htsjdk/samtools/ValidationStringency.java | 0
.../java/htsjdk/samtools/apps/TimeChannel.java | 0
.../htsjdk/samtools/apps/TimeRandomAccessFile.java | 0
src/main/java/htsjdk/samtools/cram/CRAIEntry.java | 195 +
src/main/java/htsjdk/samtools/cram/CRAIIndex.java | 267 ++
.../java/htsjdk/samtools/cram/CRAMException.java | 0
.../cram/build/CompressionHeaderFactory.java | 0
.../samtools/cram/build/ContainerFactory.java | 0
.../samtools/cram/build/ContainerParser.java | 0
.../samtools/cram/build/Cram2SamRecordFactory.java | 0
.../samtools/cram/build/CramContainerIterator.java | 0
.../java/htsjdk/samtools/cram/build/CramIO.java | 0
.../htsjdk/samtools/cram/build/CramNormalizer.java | 347 ++
.../cram/build/CramSpanContainerIterator.java | 0
.../samtools/cram/build/Sam2CramRecordFactory.java | 0
.../java/htsjdk/samtools/cram/build/Utils.java | 54 +
.../samtools/cram/common/CramVersionPolicies.java | 0
.../htsjdk/samtools/cram/common/CramVersions.java | 11 +
.../htsjdk/samtools/cram/common/IntHashMap.java | 0
.../htsjdk/samtools/cram/common/MutableInt.java | 0
.../java/htsjdk/samtools/cram/common/Version.java | 0
.../samtools/cram/digest/AbstractSerialDigest.java | 0
.../samtools/cram/digest/ByteSumCombine.java | 0
.../java/htsjdk/samtools/cram/digest/Combine.java | 0
.../samtools/cram/digest/ContentDigests.java | 0
.../htsjdk/samtools/cram/digest/Crc32Hasher.java | 0
.../samtools/cram/digest/IntegerSumCombine.java | 0
.../samtools/cram/digest/MessageDigestHasher.java | 0
.../java/htsjdk/samtools/cram/digest/SERIES.java | 0
.../samtools/cram/encoding/AbstractBitCodec.java | 0
.../samtools/cram/encoding/BetaIntegerCodec.java | 0
.../cram/encoding/BetaIntegerEncoding.java | 0
.../htsjdk/samtools/cram/encoding/BitCodec.java | 0
.../cram/encoding/ByteArrayLenEncoding.java | 0
.../cram/encoding/ByteArrayStopEncoding.java | 0
.../htsjdk/samtools/cram/encoding/DataSeries.java | 0
.../samtools/cram/encoding/DataSeriesMap.java | 0
.../samtools/cram/encoding/DataSeriesType.java | 0
.../htsjdk/samtools/cram/encoding/Encoding.java | 0
.../samtools/cram/encoding/EncodingFactory.java | 0
.../cram/encoding/ExternalByteArrayCodec.java | 0
.../cram/encoding/ExternalByteArrayEncoding.java | 0
.../samtools/cram/encoding/ExternalByteCodec.java | 0
.../cram/encoding/ExternalByteEncoding.java | 0
.../samtools/cram/encoding/ExternalCompressor.java | 0
.../cram/encoding/ExternalIntegerCodec.java | 0
.../cram/encoding/ExternalIntegerEncoding.java | 0
.../samtools/cram/encoding/ExternalLongCodec.java | 0
.../cram/encoding/ExternalLongEncoding.java | 0
.../samtools/cram/encoding/GammaIntegerCodec.java | 0
.../cram/encoding/GammaIntegerEncoding.java | 0
.../samtools/cram/encoding/GolombIntegerCodec.java | 0
.../cram/encoding/GolombIntegerEncoding.java | 0
.../samtools/cram/encoding/GolombLongCodec.java | 0
.../samtools/cram/encoding/GolombLongEncoding.java | 0
.../cram/encoding/GolombRiceIntegerCodec.java | 0
.../cram/encoding/GolombRiceIntegerEncoding.java | 0
.../htsjdk/samtools/cram/encoding/NullCodec.java | 0
.../samtools/cram/encoding/NullEncoding.java | 0
.../cram/encoding/SubexponentialIntegerCodec.java | 0
.../encoding/SubexponentialIntegerEncoding.java | 0
.../cram/encoding/huffman/HuffmanCode.java | 0
.../cram/encoding/huffman/HuffmanLeaf.java | 0
.../cram/encoding/huffman/HuffmanNode.java | 0
.../cram/encoding/huffman/HuffmanTree.java | 0
.../huffman/codec/CanonicalHuffmanByteCodec.java | 0
.../codec/CanonicalHuffmanIntegerCodec.java | 0
.../encoding/huffman/codec/HuffmanBitCode.java | 0
.../huffman/codec/HuffmanByteEncoding.java | 0
.../encoding/huffman/codec/HuffmanByteHelper.java | 0
.../encoding/huffman/codec/HuffmanIntHelper.java | 0
.../huffman/codec/HuffmanIntegerEncoding.java | 0
.../huffman/codec/HuffmanParamsCalculator.java | 0
.../samtools/cram/encoding/rans/Constants.java | 0
.../htsjdk/samtools/cram/encoding/rans/D04.java | 0
.../htsjdk/samtools/cram/encoding/rans/D14.java | 0
.../samtools/cram/encoding/rans/Decoding.java | 0
.../htsjdk/samtools/cram/encoding/rans/E04.java | 0
.../htsjdk/samtools/cram/encoding/rans/E14.java | 0
.../samtools/cram/encoding/rans/Encoding.java | 0
.../samtools/cram/encoding/rans/Frequencies.java | 0
.../htsjdk/samtools/cram/encoding/rans/RANS.java | 0
.../htsjdk/samtools/cram/encoding/rans/Utils.java | 0
.../cram/encoding/reader/AbstractReader.java | 0
.../cram/encoding/reader/CramRecordReader.java | 0
.../samtools/cram/encoding/reader/DataReader.java | 0
.../cram/encoding/reader/DataReaderFactory.java | 228 +
.../cram/encoding/reader/RefSeqIdReader.java | 0
.../encoding/readfeatures/BaseQualityScore.java | 0
.../samtools/cram/encoding/readfeatures/Bases.java | 0
.../cram/encoding/readfeatures/Deletion.java | 0
.../cram/encoding/readfeatures/HardClip.java | 0
.../cram/encoding/readfeatures/InsertBase.java | 0
.../cram/encoding/readfeatures/Insertion.java | 0
.../cram/encoding/readfeatures/Padding.java | 0
.../cram/encoding/readfeatures/ReadBase.java | 0
.../cram/encoding/readfeatures/ReadFeature.java | 0
.../cram/encoding/readfeatures/RefSkip.java | 0
.../cram/encoding/readfeatures/Scores.java | 0
.../cram/encoding/readfeatures/SoftClip.java | 0
.../cram/encoding/readfeatures/Substitution.java | 0
.../samtools/cram/encoding/writer/DataWriter.java | 0
.../cram/encoding/writer/DataWriterFactory.java | 0
.../samtools/cram/encoding/writer/Writer.java | 0
.../htsjdk/samtools/cram/io/BitInputStream.java | 0
.../htsjdk/samtools/cram/io/BitOutputStream.java | 0
.../htsjdk/samtools/cram/io/CRC32InputStream.java | 0
.../htsjdk/samtools/cram/io/CRC32OutputStream.java | 0
.../samtools/cram/io/CountingInputStream.java | 0
.../java/htsjdk/samtools/cram/io/CramArray.java | 0
.../java/htsjdk/samtools/cram/io/CramInt.java | 0
.../samtools/cram/io/DefaultBitInputStream.java | 0
.../samtools/cram/io/DefaultBitOutputStream.java | 0
.../cram/io/ExposedByteArrayOutputStream.java | 0
.../samtools/cram/io/ExternalCompression.java | 152 +
.../java/htsjdk/samtools/cram/io/ITF8.java | 0
.../htsjdk/samtools/cram/io/InputStreamUtils.java | 0
.../java/htsjdk/samtools/cram/io/LTF8.java | 0
.../htsjdk/samtools/cram/lossy/BaseCategory.java | 0
.../samtools/cram/lossy/BaseCategoryType.java | 0
.../java/htsjdk/samtools/cram/lossy/Binning.java | 0
.../samtools/cram/lossy/PreservationPolicy.java | 0
.../cram/lossy/QualityScorePreservation.java | 0
.../samtools/cram/lossy/QualityScoreTreatment.java | 0
.../cram/lossy/QualityScoreTreatmentType.java | 0
.../htsjdk/samtools/cram/lossy/ReadCategory.java | 0
.../samtools/cram/lossy/ReadCategoryType.java | 0
.../samtools/cram/ref/CRAMReferenceSource.java | 22 +
.../htsjdk/samtools/cram/ref/EnaRefService.java | 0
.../cram/ref/InMemoryReferenceSequenceFile.java | 0
.../htsjdk/samtools/cram/ref/ReferenceRegion.java | 0
.../htsjdk/samtools/cram/ref/ReferenceSource.java | 280 ++
.../htsjdk/samtools/cram/ref/ReferenceTracks.java | 0
.../samtools/cram/structure/AlignmentSpan.java | 0
.../java/htsjdk/samtools/cram/structure/Block.java | 0
.../cram/structure/BlockCompressionMethod.java | 0
.../samtools/cram/structure/BlockContentType.java | 0
.../samtools/cram/structure/CompressionHeader.java | 299 ++
.../htsjdk/samtools/cram/structure/Container.java | 0
.../samtools/cram/structure/ContainerHeaderIO.java | 96 +
.../samtools/cram/structure/ContainerIO.java | 0
.../cram/structure/CramCompressionRecord.java | 0
.../htsjdk/samtools/cram/structure/CramHeader.java | 0
.../htsjdk/samtools/cram/structure/EncodingID.java | 0
.../samtools/cram/structure/EncodingKey.java | 0
.../samtools/cram/structure/EncodingParams.java | 0
.../htsjdk/samtools/cram/structure/ReadTag.java | 0
.../java/htsjdk/samtools/cram/structure/Slice.java | 245 +
.../htsjdk/samtools/cram/structure/SliceIO.java | 0
.../cram/structure/SubstitutionMatrix.java | 0
.../htsjdk/samtools/example/ExampleSamUsage.java | 0
.../htsjdk/samtools/example/PrintReadsExample.java | 98 +
.../htsjdk/samtools/fastq/AsyncFastqWriter.java | 0
.../htsjdk/samtools/fastq/BasicFastqWriter.java | 0
.../java/htsjdk/samtools/fastq/FastqConstants.java | 0
.../java/htsjdk/samtools/fastq/FastqReader.java | 0
.../java/htsjdk/samtools/fastq/FastqRecord.java | 0
.../java/htsjdk/samtools/fastq/FastqWriter.java | 0
.../htsjdk/samtools/fastq/FastqWriterFactory.java | 31 +
.../samtools/filter/AbstractJavascriptFilter.java | 0
.../htsjdk/samtools/filter/AggregateFilter.java | 0
.../java/htsjdk/samtools/filter/AlignedFilter.java | 0
.../samtools/filter/DuplicateReadFilter.java | 0
.../filter/FailsVendorReadQualityFilter.java | 0
.../htsjdk/samtools/filter/FilteringIterator.java | 53 +
.../samtools/filter/FilteringSamIterator.java | 155 +
.../htsjdk/samtools/filter/InsertSizeFilter.java | 0
.../htsjdk/samtools/filter/IntervalFilter.java | 102 +
.../samtools/filter/IntervalKeepPairFilter.java | 108 +
.../samtools/filter/JavascriptSamRecordFilter.java | 0
.../samtools/filter/MappingQualityFilter.java | 0
.../samtools/filter/NotPrimaryAlignmentFilter.java | 0
.../samtools/filter/OverclippedReadFilter.java | 0
.../htsjdk/samtools/filter/ReadNameFilter.java | 0
.../htsjdk/samtools/filter/SamRecordFilter.java | 0
.../samtools/filter/SecondaryAlignmentFilter.java | 0
.../filter/SecondaryOrSupplementaryFilter.java | 0
.../htsjdk/samtools/filter/SolexaNoiseFilter.java | 0
.../java/htsjdk/samtools/filter/TagFilter.java | 0
.../samtools/filter/WholeReadClippedFilter.java | 0
.../java/htsjdk/samtools/liftover/Chain.java | 0
.../java/htsjdk/samtools/liftover/LiftOver.java | 319 ++
.../java/htsjdk/samtools/metrics/Header.java | 0
.../java/htsjdk/samtools/metrics/MetricBase.java | 0
.../java/htsjdk/samtools/metrics/MetricsFile.java | 594 +++
.../java/htsjdk/samtools/metrics/StringHeader.java | 0
.../htsjdk/samtools/metrics/VersionHeader.java | 0
.../reference/AbstractFastaSequenceFile.java | 0
.../samtools/reference/FastaSequenceFile.java | 0
.../samtools/reference/FastaSequenceIndex.java | 0
.../reference/IndexedFastaSequenceFile.java | 0
.../samtools/reference/ReferenceSequence.java | 84 +
.../samtools/reference/ReferenceSequenceFile.java | 0
.../reference/ReferenceSequenceFileFactory.java | 0
.../reference/ReferenceSequenceFileWalker.java | 0
.../seekablestream/ByteArraySeekableStream.java | 99 +
.../seekablestream/ISeekableStreamFactory.java | 0
.../seekablestream/SeekableBufferedStream.java | 0
.../samtools/seekablestream/SeekableFTPStream.java | 0
.../seekablestream/SeekableFTPStreamHelper.java | 0
.../seekablestream/SeekableFileStream.java | 0
.../seekablestream/SeekableHTTPStream.java | 0
.../seekablestream/SeekableMemoryStream.java | 64 +
.../seekablestream/SeekablePathStream.java | 121 +
.../samtools/seekablestream/SeekableStream.java | 0
.../seekablestream/SeekableStreamFactory.java | 97 +
.../samtools/seekablestream/UserPasswordInput.java | 0
.../java/htsjdk/samtools/sra/ReferenceCache.java | 46 +
.../java/htsjdk/samtools/sra/SRAAccession.java | 177 +
.../htsjdk/samtools/sra/SRAAlignmentIterator.java | 209 +
.../samtools/sra/SRAIndexedSequenceFile.java | 112 +
.../java/htsjdk/samtools/sra/SRALazyRecord.java | 0
.../samtools/sra/SRAUnalignmentIterator.java | 0
.../java/htsjdk/samtools/sra/SRAUtils.java | 0
.../htsjdk/samtools/util/AbstractAsyncWriter.java | 137 +
.../htsjdk/samtools/util/AbstractIterator.java | 0
.../htsjdk/samtools/util/AbstractLocusInfo.java | 146 +
.../samtools/util/AbstractLocusIterator.java | 572 +++
.../samtools/util/AbstractProgressLogger.java | 0
.../samtools/util/AbstractRecordAndOffset.java | 130 +
.../java/htsjdk/samtools/util/AsciiWriter.java | 0
.../samtools/util/AsyncBufferedIterator.java | 281 ++
.../java/htsjdk/samtools/util/BinaryCodec.java | 0
.../util/BlockCompressedFilePointerUtil.java | 0
.../samtools/util/BlockCompressedInputStream.java | 513 ++
.../samtools/util/BlockCompressedOutputStream.java | 392 ++
.../util/BlockCompressedStreamConstants.java | 0
.../java/htsjdk/samtools/util/BlockGunzipper.java | 132 +
.../htsjdk/samtools/util/BufferedLineReader.java | 0
.../java/htsjdk/samtools/util/CigarUtil.java | 0
.../htsjdk/samtools/util/CloseableIterator.java | 63 +
.../java/htsjdk/samtools/util/CloserUtil.java | 0
.../java/htsjdk/samtools/util/CodeUtil.java | 0
.../java/htsjdk/samtools/util/CollectionUtil.java | 191 +
.../java/htsjdk/samtools/util/ComparableTuple.java | 0
.../java/htsjdk/samtools/util/CoordMath.java | 0
.../htsjdk/samtools/util/CoordSpanInputSteam.java | 0
.../samtools/util/CustomGzipOutputStream.java | 24 +
.../java/htsjdk/samtools/util/DateParser.java | 0
.../htsjdk/samtools/util/DelegatingIterator.java | 0
.../java/htsjdk/samtools/util/DiskBackedQueue.java | 0
.../htsjdk/samtools/util/EdgeReadIterator.java | 228 +
.../samtools/util/EdgingRecordAndOffset.java | 219 +
.../java/htsjdk/samtools/util/FastLineReader.java | 0
.../htsjdk/samtools/util/FastqQualityFormat.java | 0
.../samtools/util/FileAppendStreamLRUCache.java | 0
.../java/htsjdk/samtools/util/FormatUtil.java | 0
src/main/java/htsjdk/samtools/util/Histogram.java | 567 +++
.../java/htsjdk/samtools/util/HttpUtils.java | 0
src/main/java/htsjdk/samtools/util/IOUtil.java | 946 ++++
.../java/htsjdk/samtools/util/Interval.java | 0
.../java/htsjdk/samtools/util/IntervalList.java | 790 ++++
.../util/IntervalListReferenceSequenceMask.java | 0
.../java/htsjdk/samtools/util/IntervalTree.java | 0
.../java/htsjdk/samtools/util/IntervalTreeMap.java | 0
.../java/htsjdk/samtools/util/IntervalUtil.java | 0
.../java/htsjdk/samtools/util/Iso8601Date.java | 0
.../java/htsjdk/samtools/util/IterableAdapter.java | 0
.../htsjdk/samtools/util/IterableOnceIterator.java | 0
.../java/htsjdk/samtools/util/Iterables.java | 0
src/main/java/htsjdk/samtools/util/Lazy.java | 40 +
.../java/htsjdk/samtools/util/LineReader.java | 0
.../java/htsjdk/samtools/util/ListMap.java | 0
.../java/htsjdk/samtools/util/Locatable.java | 0
.../java/htsjdk/samtools/util/LocationAware.java | 0
.../java/htsjdk/samtools/util/Locus.java | 0
.../java/htsjdk/samtools/util/LocusComparator.java | 0
.../java/htsjdk/samtools/util/LocusImpl.java | 0
src/main/java/htsjdk/samtools/util/Log.java | 214 +
.../samtools/util/Md5CalculatingInputStream.java | 0
.../samtools/util/Md5CalculatingOutputStream.java | 0
.../java/htsjdk/samtools/util/MergingIterator.java | 0
.../java/htsjdk/samtools/util/Murmur3.java | 0
.../java/htsjdk/samtools/util/OverlapDetector.java | 193 +
.../java/htsjdk/samtools/util/PeekIterator.java | 0
.../htsjdk/samtools/util/PeekableIterator.java | 0
.../samtools/util/PositionalOutputStream.java | 65 +
.../java/htsjdk/samtools/util/ProcessExecutor.java | 0
.../java/htsjdk/samtools/util/ProgressLogger.java | 0
.../samtools/util/ProgressLoggerInterface.java | 0
.../samtools/util/QualityEncodingDetector.java | 405 ++
.../java/htsjdk/samtools/util/QualityUtil.java | 0
.../samtools/util/ReferenceSequenceMask.java | 0
.../htsjdk/samtools/util/RelativeIso8601Date.java | 0
.../htsjdk/samtools/util/ResourceLimitedMap.java | 0
.../samtools/util/ResourceLimitedMapFunctor.java | 0
.../htsjdk/samtools/util/RuntimeEOFException.java | 0
.../htsjdk/samtools/util/RuntimeIOException.java | 0
.../samtools/util/RuntimeScriptException.java | 0
.../htsjdk/samtools/util/SamLocusIterator.java | 292 ++
.../util/SamRecordIntervalIteratorFactory.java | 157 +
.../samtools/util/SamRecordTrackingBuffer.java | 0
.../htsjdk/samtools/util/SamRecordWithOrdinal.java | 0
.../java/htsjdk/samtools/util/SequenceUtil.java | 1031 ++++
.../java/htsjdk/samtools/util/SnappyLoader.java | 0
.../samtools/util/SolexaQualityConverter.java | 0
.../htsjdk/samtools/util/SortingCollection.java | 514 ++
.../samtools/util/SortingLongCollection.java | 0
.../java/htsjdk/samtools/util/StopWatch.java | 0
.../htsjdk/samtools/util/StringLineReader.java | 0
src/main/java/htsjdk/samtools/util/StringUtil.java | 603 +++
.../htsjdk/samtools/util/TempStreamFactory.java | 0
src/main/java/htsjdk/samtools/util/TestUtil.java | 98 +
.../java/htsjdk/samtools/util/TrimmingUtil.java | 0
src/main/java/htsjdk/samtools/util/Tuple.java | 41 +
.../util/WholeGenomeReferenceSequenceMask.java | 0
.../java/htsjdk/samtools/util/ftp/FTPClient.java | 0
.../java/htsjdk/samtools/util/ftp/FTPReply.java | 0
.../java/htsjdk/samtools/util/ftp/FTPStream.java | 0
.../java/htsjdk/samtools/util/ftp/FTPUtils.java | 0
.../htsjdk/samtools/util/zip/DeflaterFactory.java | 48 +
.../java/htsjdk/tribble/AbstractFeatureCodec.java | 0
.../java/htsjdk/tribble/AbstractFeatureReader.java | 193 +
.../java/htsjdk/tribble/AsciiFeatureCodec.java | 92 +
.../java/htsjdk/tribble/BinaryFeatureCodec.java | 52 +
.../htsjdk/tribble/CloseableTribbleIterator.java | 0
src/main/java/htsjdk/tribble/Feature.java | 43 +
src/main/java/htsjdk/tribble/FeatureCodec.java | 136 +
.../java/htsjdk/tribble/FeatureCodecHeader.java | 0
.../java/htsjdk/tribble/FeatureReader.java | 0
.../java/htsjdk/tribble/NameAwareCodec.java | 0
src/main/java/htsjdk/tribble/SimpleFeature.java | 53 +
.../java/htsjdk/tribble/TabixFeatureReader.java | 217 +
src/{ => main}/java/htsjdk/tribble/Tribble.java | 0
.../java/htsjdk/tribble/TribbleException.java | 0
.../tribble/TribbleIndexedFeatureReader.java | 573 +++
.../java/htsjdk/tribble/annotation/Strand.java | 0
src/main/java/htsjdk/tribble/bed/BEDCodec.java | 242 +
.../java/htsjdk/tribble/bed/BEDFeature.java | 0
.../java/htsjdk/tribble/bed/FullBEDFeature.java | 0
.../java/htsjdk/tribble/bed/SimpleBEDFeature.java | 140 +
.../java/htsjdk/tribble/example/CountRecords.java | 200 +
.../htsjdk/tribble/example/ExampleBinaryCodec.java | 128 +
.../java/htsjdk/tribble/example/IndexToTable.java | 0
.../htsjdk/tribble/example/IndicesAreEqual.java | 0
.../tribble/example/ProfileIndexReading.java | 0
.../exception/CodecLineParsingException.java | 0
.../tribble/exception/UnsortedFileException.java | 0
.../htsjdk/tribble/gelitext/DiploidGenotype.java | 0
.../htsjdk/tribble/gelitext/GeliTextCodec.java | 0
.../htsjdk/tribble/gelitext/GeliTextFeature.java | 148 +
.../java/htsjdk/tribble/index/AbstractIndex.java | 451 ++
.../java/htsjdk/tribble/index/Block.java | 0
.../java/htsjdk/tribble/index/ChrIndex.java | 0
.../htsjdk/tribble/index/DynamicIndexCreator.java | 0
src/main/java/htsjdk/tribble/index/Index.java | 99 +
.../java/htsjdk/tribble/index/IndexCreator.java | 57 +
.../java/htsjdk/tribble/index/IndexFactory.java | 515 ++
.../java/htsjdk/tribble/index/MutableIndex.java | 0
.../htsjdk/tribble/index/TribbleIndexCreator.java | 53 +
.../htsjdk/tribble/index/interval/Interval.java | 0
.../index/interval/IntervalIndexCreator.java | 159 +
.../tribble/index/interval/IntervalTree.java | 0
.../tribble/index/interval/IntervalTreeIndex.java | 0
.../htsjdk/tribble/index/linear/LinearIndex.java | 0
.../tribble/index/linear/LinearIndexCreator.java | 126 +
.../htsjdk/tribble/index/tabix/TabixFormat.java | 0
.../htsjdk/tribble/index/tabix/TabixIndex.java | 366 ++
.../tribble/index/tabix/TabixIndexCreator.java | 202 +
.../htsjdk/tribble/readers/AsciiLineReader.java | 0
.../tribble/readers/AsciiLineReaderIterator.java | 0
.../java/htsjdk/tribble/readers/LineIterator.java | 0
.../htsjdk/tribble/readers/LineIteratorImpl.java | 0
.../java/htsjdk/tribble/readers/LineReader.java | 0
.../htsjdk/tribble/readers/LineReaderUtil.java | 56 +
.../tribble/readers/LongLineBufferedReader.java | 0
.../java/htsjdk/tribble/readers/Positional.java | 0
.../tribble/readers/PositionalBufferedStream.java | 0
.../tribble/readers/SynchronousLineReader.java | 61 +
.../tribble/readers/TabixIteratorLineReader.java | 0
.../java/htsjdk/tribble/readers/TabixReader.java | 0
src/{ => main}/java/htsjdk/tribble/readme.txt | 0
.../java/htsjdk/tribble/util/FTPHelper.java | 0
.../java/htsjdk/tribble/util/HTTPHelper.java | 0
.../tribble/util/LittleEndianInputStream.java | 0
.../tribble/util/LittleEndianOutputStream.java | 0
.../java/htsjdk/tribble/util/MathUtils.java | 0
.../java/htsjdk/tribble/util/ParsingUtils.java | 0
.../java/htsjdk/tribble/util/RemoteURLHelper.java | 0
.../java/htsjdk/tribble/util/TabixUtils.java | 0
.../java/htsjdk/tribble/util/URLHelper.java | 0
.../java/htsjdk/tribble/util/ftp/.gitignore | 0
.../util/popgen/HardyWeinbergCalculation.java | 0
src/main/java/htsjdk/variant/bcf2/BCF2Codec.java | 491 ++
.../java/htsjdk/variant/bcf2/BCF2Decoder.java | 0
.../variant/bcf2/BCF2GenotypeFieldDecoders.java | 0
.../variant/bcf2/BCF2LazyGenotypesDecoder.java | 0
.../java/htsjdk/variant/bcf2/BCF2Type.java | 0
.../java/htsjdk/variant/bcf2/BCF2Utils.java | 0
.../java/htsjdk/variant/bcf2/BCFVersion.java | 0
.../variant/example/PrintVariantsExample.java | 103 +
.../java/htsjdk/variant/utils/GeneralUtils.java | 0
.../utils/SAMSequenceDictionaryExtractor.java | 0
.../java/htsjdk/variant/variantcontext/Allele.java | 0
.../htsjdk/variant/variantcontext/CommonInfo.java | 341 ++
.../variant/variantcontext/FastGenotype.java | 173 +
.../htsjdk/variant/variantcontext/Genotype.java | 670 +++
.../variant/variantcontext/GenotypeBuilder.java | 421 ++
.../variantcontext/GenotypeJEXLContext.java | 59 +
.../variantcontext/GenotypeLikelihoods.java | 0
.../variant/variantcontext/GenotypeType.java | 0
.../variant/variantcontext/GenotypesContext.java | 0
.../htsjdk/variant/variantcontext/JEXLMap.java | 228 +
.../variantcontext/JexlMissingValueTreatment.java | 39 +
.../variantcontext/LazyGenotypesContext.java | 0
.../variantcontext/StructuralVariantType.java | 47 +
.../variant/variantcontext/VariantContext.java | 1734 +++++++
.../variantcontext/VariantContextBuilder.java | 498 ++
.../variantcontext/VariantContextComparator.java | 105 +
.../variantcontext/VariantContextUtils.java | 483 ++
.../variant/variantcontext/VariantJEXLContext.java | 102 +
.../variantcontext/filter/CompoundFilter.java | 0
.../variantcontext/filter/FilteringIterator.java | 47 +
.../filter/FilteringVariantContextIterator.java | 127 +
.../filter/GenotypeQualityFilter.java | 0
.../filter/HeterozygosityFilter.java | 0
.../filter/JavascriptVariantFilter.java | 0
.../filter/PassingVariantFilter.java | 0
.../variant/variantcontext/filter/SnpFilter.java | 0
.../filter/VariantContextFilter.java | 0
.../writer/AsyncVariantContextWriter.java | 0
.../variant/variantcontext/writer/BCF2Encoder.java | 0
.../variantcontext/writer/BCF2FieldEncoder.java | 0
.../variantcontext/writer/BCF2FieldWriter.java | 323 ++
.../writer/BCF2FieldWriterManager.java | 0
.../variant/variantcontext/writer/BCF2Writer.java | 443 ++
.../writer/IndexingVariantContextWriter.java | 180 +
.../writer/IntGenotypeFieldAccessors.java | 0
.../variant/variantcontext/writer/Options.java | 0
.../writer/SortingVariantContextWriter.java | 0
.../writer/SortingVariantContextWriterBase.java | 201 +
.../variant/variantcontext/writer/VCFWriter.java | 0
.../writer/VariantContextWriter.java | 0
.../writer/VariantContextWriterBuilder.java | 537 +++
.../writer/VariantContextWriterFactory.java | 282 ++
.../java/htsjdk/variant/vcf/AbstractVCFCodec.java | 791 ++++
.../java/htsjdk/variant/vcf/VCF3Codec.java | 0
.../java/htsjdk/variant/vcf/VCFCodec.java | 0
.../htsjdk/variant/vcf/VCFCompoundHeaderLine.java | 0
src/main/java/htsjdk/variant/vcf/VCFConstants.java | 130 +
.../htsjdk/variant/vcf/VCFContigHeaderLine.java | 0
src/main/java/htsjdk/variant/vcf/VCFEncoder.java | 382 ++
.../java/htsjdk/variant/vcf/VCFFileReader.java | 153 +
.../htsjdk/variant/vcf/VCFFilterHeaderLine.java | 79 +
.../htsjdk/variant/vcf/VCFFormatHeaderLine.java | 0
.../java/htsjdk/variant/vcf/VCFHeader.java | 0
.../java/htsjdk/variant/vcf/VCFHeaderLine.java | 0
.../htsjdk/variant/vcf/VCFHeaderLineCount.java | 0
.../variant/vcf/VCFHeaderLineTranslator.java | 183 +
.../java/htsjdk/variant/vcf/VCFHeaderLineType.java | 0
.../java/htsjdk/variant/vcf/VCFHeaderVersion.java | 0
.../java/htsjdk/variant/vcf/VCFIDHeaderLine.java | 0
.../java/htsjdk/variant/vcf/VCFInfoHeaderLine.java | 0
.../java/htsjdk/variant/vcf/VCFRecordCodec.java | 0
.../htsjdk/variant/vcf/VCFSimpleHeaderLine.java | 0
.../htsjdk/variant/vcf/VCFStandardHeaderLines.java | 233 +
.../java/htsjdk/variant/vcf/VCFUtils.java | 0
src/scripts/build_intel_deflater.sh | 73 -
.../htsjdk/cram/io/ExternalCompressionTest.java | 30 +
.../htsjdk/samtools/AbstractBAMFileIndexTest.java | 0
.../java/htsjdk/samtools/BAMCigarOverflowTest.java | 29 +
.../java/htsjdk/samtools/BAMFileIndexTest.java | 527 +++
.../java/htsjdk/samtools/BAMFileWriterTest.java | 192 +
.../java/htsjdk/samtools/BAMIndexWriterTest.java | 227 +
src/test/java/htsjdk/samtools/BAMIteratorTest.java | 71 +
...AMQueryMultipleIntervalsIteratorFilterTest.java | 146 +
.../java/htsjdk/samtools/BAMRemoteFileTest.java | 327 ++
.../java/htsjdk/samtools/BinTest.java | 0
.../java/htsjdk/samtools/CRAMBAIIndexerTest.java | 87 +
.../java/htsjdk/samtools/CRAMCRAIIndexerTest.java | 183 +
.../java/htsjdk/samtools/CRAMComplianceTest.java | 150 +
.../samtools/CRAMContainerStreamWriterTest.java | 184 +
.../java/htsjdk/samtools/CRAMEdgeCasesTest.java | 158 +
.../java/htsjdk/samtools/CRAMFileBAIIndexTest.java | 301 ++
.../htsjdk/samtools/CRAMFileCRAIIndexTest.java | 368 ++
.../java/htsjdk/samtools/CRAMFileReaderTest.java | 231 +
.../java/htsjdk/samtools/CRAMFileWriterTest.java | 282 ++
.../samtools/CRAMFileWriterWithIndexTest.java | 209 +
.../java/htsjdk/samtools/CRAMIndexQueryTest.java | 708 +++
.../java/htsjdk/samtools/ChunkTest.java | 0
.../java/htsjdk/samtools/CigarCodecTest.java | 0
.../java/htsjdk/samtools/CigarTest.java | 0
.../htsjdk/samtools/DownsamplingIteratorTests.java | 87 +
.../htsjdk/samtools/DuplicateSetIteratorTest.java | 0
.../java/htsjdk/samtools/GenomicIndexUtilTest.java | 50 +
...MergingSamRecordIteratorGroupCollisionTest.java | 0
.../samtools/MergingSamRecordIteratorTest.java | 0
.../htsjdk/samtools/ProgramRecordChainingTest.java | 0
.../samtools/SAMBinaryTagAndValueUnitTest.java | 183 +
.../java/htsjdk/samtools/SAMCloneTest.java | 0
.../htsjdk/samtools/SAMFileWriterFactoryTest.java | 307 ++
.../java/htsjdk/samtools/SAMFlagTest.java | 0
.../java/htsjdk/samtools/SAMIntegerTagTest.java | 375 ++
.../samtools/SAMRecordDuplicateComparatorTest.java | 0
.../java/htsjdk/samtools/SAMRecordUnitTest.java | 1041 ++++
.../samtools/SAMSequenceDictionaryCodecTest.java | 122 +
.../htsjdk/samtools/SAMSequenceDictionaryTest.java | 147 +
.../java/htsjdk/samtools/SAMTextReaderTest.java | 0
.../java/htsjdk/samtools/SAMTextWriterTest.java | 130 +
src/test/java/htsjdk/samtools/SAMUtilsTest.java | 250 +
.../htsjdk/samtools/SamFileHeaderMergerTest.java | 265 ++
src/test/java/htsjdk/samtools/SamFilesTest.java | 91 +
.../java/htsjdk/samtools/SamFlagFieldTest.java | 150 +
.../samtools/SamHeaderRecordComparatorTest.java | 0
src/test/java/htsjdk/samtools/SamIndexesTest.java | 193 +
.../java/htsjdk/samtools/SamPairUtilTest.java | 0
.../java/htsjdk/samtools/SamReaderFactoryTest.java | 468 ++
.../java/htsjdk/samtools/SamReaderSortTest.java | 102 +
src/test/java/htsjdk/samtools/SamReaderTest.java | 170 +
src/test/java/htsjdk/samtools/SamSpecIntTest.java | 97 +
src/test/java/htsjdk/samtools/SamStreamsTest.java | 124 +
.../SequenceNameTruncationAndValidationTest.java | 98 +
.../java/htsjdk/samtools/ValidateSamFileTest.java | 547 +++
.../java/htsjdk/samtools/apps/.gitignore | 0
.../java/htsjdk/samtools/cram/CRAIEntryTest.java | 144 +
.../java/htsjdk/samtools/cram/CRAIIndexTest.java | 220 +
.../samtools/cram/LosslessRoundTripTest.java | 0
.../java/htsjdk/samtools/cram/VersionTest.java | 106 +
.../cram/build/CompressionHeaderFactoryTest.java | 0
.../samtools/cram/build/ContainerFactoryTest.java | 0
.../samtools/cram/build/ContainerParserTest.java | 0
.../htsjdk/samtools/cram/build/CramIOTest.java | 0
.../cram/encoding/huffman/codec/HuffmanTest.java | 0
.../samtools/cram/encoding/rans/RansTest.java | 0
.../java/htsjdk/samtools/cram/io/ITF8Test.java | 0
.../java/htsjdk/samtools/cram/io/LTF8Test.java | 0
.../cram/lossy/QualityScorePreservationTest.java | 0
.../samtools/cram/ref/EnaRefServiceTest.java | 0
.../cram/structure/CramCompressionRecordTest.java | 0
.../samtools/cram/structure/ReadTagTest.java | 0
.../htsjdk/samtools/cram/structure/SliceTests.java | 70 +
.../cram/structure/SubstitutionMatrixTest.java | 0
.../java/htsjdk/samtools/fastq/.gitignore | 0
.../htsjdk/samtools/fastq/FastqRecordTest.java | 204 +
.../htsjdk/samtools/fastq/FastqWriterTest.java | 73 +
.../filter/FailsVendorReadQualityFilterTest.java | 0
.../samtools/filter/InsertSizeFilterTest.java | 0
.../filter/IntervalKeepPairFilterTest.java | 123 +
.../filter/JavascriptSamRecordFilterTest.java | 74 +
.../samtools/filter/MappingQualityFilterTest.java | 0
.../samtools/filter/OverclippedReadFilterTest.java | 0
.../samtools/filter/SolexaNoiseFilterTest.java | 0
.../java/htsjdk/samtools/filter/TagFilterTest.java | 0
.../htsjdk/samtools/liftover/LiftOverTest.java | 468 ++
.../htsjdk/samtools/metrics/MetricBaseTest.java | 0
.../htsjdk/samtools/metrics/MetricsFileTest.java | 213 +
.../htsjdk/samtools/metrics/StringHeaderTest.java | 0
.../htsjdk/samtools/metrics/VersionHeaderTest.java | 0
.../reference/FakeReferenceSequenceFile.java | 0
.../samtools/reference/FastaSequenceFileTest.java | 85 +
.../samtools/reference/FastaSequenceIndexTest.java | 256 +
.../reference/InMemoryReferenceSequenceFile.java | 0
.../reference/IndexedFastaSequenceFileTest.java | 308 ++
.../ReferenceSequenceFileFactoryTests.java | 39 +
.../reference/ReferenceSequenceFileWalkerTest.java | 73 +
.../samtools/reference/ReferenceSequenceTests.java | 0
.../seekablestream/SeekableBufferedStreamTest.java | 162 +
.../seekablestream/SeekableFTPStreamTest.java | 0
.../seekablestream/SeekableFileStreamTest.java | 52 +
.../seekablestream/SeekableMemoryStreamTest.java | 93 +
.../seekablestream/SeekablePathStreamTest.java | 51 +
.../seekablestream/SeekableStreamFactoryTest.java | 45 +
.../java/htsjdk/samtools/sra/AbstractSRATest.java | 89 +
.../java/htsjdk/samtools/sra/SRAAccessionTest.java | 28 +
.../java/htsjdk/samtools/sra/SRAIndexTest.java | 134 +
.../htsjdk/samtools/sra/SRALazyRecordTest.java | 51 +
.../java/htsjdk/samtools/sra/SRAQueryTest.java | 0
.../java/htsjdk/samtools/sra/SRAReferenceTest.java | 95 +
src/test/java/htsjdk/samtools/sra/SRATest.java | 434 ++
.../samtools/util/AbstractLocusInfoTest.java | 79 +
.../util/AbstractLocusIteratorTestTemplate.java | 68 +
.../samtools/util/AbstractRecordAndOffsetTest.java | 63 +
.../samtools/util/AsyncBufferedIteratorTest.java | 115 +
.../java/htsjdk/samtools/util/AsyncWriterTest.java | 77 +
.../java/htsjdk/samtools/util/BinaryCodecTest.java | 0
.../util/BlockCompressedFilePointerUtilTest.java | 0
.../util/BlockCompressedOutputStreamTest.java | 214 +
.../util/BlockCompressedTerminatorTest.java | 59 +
.../java/htsjdk/samtools/util/CigarUtilTest.java | 0
.../samtools/util/CloseableIteratorTest.java | 31 +
.../java/htsjdk/samtools/util/CodeUtilTest.java | 0
.../htsjdk/samtools/util/ComparableTupleTest.java | 0
.../samtools/util/CoordSpanInputSteamTest.java | 0
.../htsjdk/samtools/util/DiskBackedQueueTest.java | 0
.../htsjdk/samtools/util/EdgeReadIteratorTest.java | 402 ++
.../samtools/util/EdgingRecordAndOffsetTest.java | 94 +
.../java/htsjdk/samtools/util/HistogramTest.java | 366 ++
.../htsjdk/samtools/util/IntervalListTest.java | 520 ++
.../htsjdk/samtools/util/IntervalTreeMapTest.java | 0
.../htsjdk/samtools/util/IntervalTreeTest.java | 0
src/test/java/htsjdk/samtools/util/IoUtilTest.java | 190 +
.../java/htsjdk/samtools/util/Iso8601DateTest.java | 0
.../java/htsjdk/samtools/util/IupacTest.java | 0
.../htsjdk/samtools/util/MergingIteratorTest.java | 0
.../htsjdk/samtools/util/OverlapDetectorTest.java | 240 +
.../samtools/util/PositionalOutputStreamTest.java | 62 +
.../samtools/util/QualityEncodingDetectorTest.java | 109 +
.../samtools/util/RelativeIso8601DateTest.java | 53 +
.../htsjdk/samtools/util/SamLocusIteratorTest.java | 673 +++
.../htsjdk/samtools/util/SequenceUtilTest.java | 453 ++
.../samtools/util/SolexaQualityConverterTest.java | 0
.../samtools/util/SortingCollectionTest.java | 0
.../samtools/util/SortingLongCollectionTest.java | 0
.../htsjdk/samtools/util/StringLineReaderTest.java | 0
.../java/htsjdk/samtools/util/StringUtilTest.java | 122 +
.../htsjdk/samtools/util/TrimmingUtilTest.java | 0
.../java/htsjdk/samtools/util/TupleTest.java | 0
.../htsjdk/tribble/AbstractFeatureReaderTest.java | 112 +
.../java/htsjdk/tribble/BinaryFeaturesTest.java | 62 +
.../java/htsjdk/tribble/FeatureReaderTest.java | 168 +
src/test/java/htsjdk/tribble/TestUtils.java | 28 +
.../tribble/TribbleIndexFeatureReaderTest.java | 88 +
.../java/htsjdk/tribble/TribbleTest.java | 0
src/test/java/htsjdk/tribble/bed/BEDCodecTest.java | 240 +
.../java/htsjdk/tribble/gelitext/GeliTextTest.java | 100 +
.../htsjdk/tribble/index/IndexFactoryTest.java | 120 +
src/test/java/htsjdk/tribble/index/IndexTest.java | 97 +
.../tribble/index/interval/IntervalTreeTest.java | 0
.../tribble/index/linear/LinearIndexTest.java | 0
.../htsjdk/tribble/index/tabix/TabixIndexTest.java | 144 +
.../tribble/readers/AsciiLineReaderTest.java | 0
.../readers/LongLineBufferedReaderTest.java | 0
.../readers/PositionalBufferedStreamTest.java | 0
.../java/htsjdk/tribble/readers/ReaderTest.java | 0
.../readers/SynchronousLineReaderUnitTest.java | 39 +
.../htsjdk/tribble/readers/TabixReaderTest.java | 162 +
.../java/htsjdk/tribble/source/.gitignore | 0
.../java/htsjdk/tribble/util/ParsingUtilsTest.java | 0
.../htsjdk/tribble/util/ftp/FTPClientTest.java | 0
.../java/htsjdk/tribble/util/ftp/FTPUtilsTest.java | 0
.../util/popgen/HardyWeinbergCalculationTest.java | 0
.../htsjdk/variant/PrintVariantsExampleTest.java | 65 +
src/test/java/htsjdk/variant/VariantBaseTest.java | 278 ++
.../variant/bcf2/BCF2EncoderDecoderUnitTest.java | 0
.../htsjdk/variant/bcf2/BCF2UtilsUnitTest.java | 0
.../utils/SAMSequenceDictionaryExtractorTest.java | 65 +
.../variant/variantcontext/AlleleUnitTest.java | 0
.../variantcontext/GenotypeBuilderTest.java | 75 +
.../GenotypeLikelihoodsUnitTest.java | 337 ++
.../variant/variantcontext/GenotypeUnitTest.java | 107 +
.../variantcontext/GenotypesContextUnitTest.java | 0
.../variantcontext/VariantContextBuilderTest.java | 0
.../variantcontext/VariantContextTestProvider.java | 1014 ++++
.../variantcontext/VariantContextUnitTest.java | 1621 +++++++
.../variantcontext/VariantJEXLContextUnitTest.java | 312 ++
.../variantcontext/filter/AllFailFilter.java | 0
.../variantcontext/filter/AllPassFilter.java | 0
.../variantcontext/filter/CompoundFilterTest.java | 0
.../FilteringVariantContextIteratorTest.java | 88 +
.../filter/GenotypeQualityFilterTest.java | 0
.../filter/HeterozygosityFilterTest.java | 128 +
.../filter/JavascriptVariantFilterTest.java | 72 +
.../filter/PassingVariantFilterTest.java | 0
.../variantcontext/filter/SnpFilterTest.java | 0
.../writer/TabixOnTheFlyIndexCreationTest.java | 66 +
.../variantcontext/writer/VCFWriterUnitTest.java | 280 ++
.../VariantContextWriterBuilderUnitTest.java | 399 ++
.../writer/VariantContextWritersUnitTest.java | 0
.../htsjdk/variant/vcf/AbstractVCFCodecTest.java | 60 +
.../htsjdk/variant/vcf/IndexFactoryUnitTest.java | 0
.../variant/vcf/VCFCompoundHeaderLineUnitTest.java | 0
.../java/htsjdk/variant/vcf/VCFEncoderTest.java | 0
.../vcf/VCFHeaderLineTranslatorUnitTest.java | 62 +
.../htsjdk/variant/vcf/VCFHeaderLineUnitTest.java | 0
.../java/htsjdk/variant/vcf/VCFHeaderUnitTest.java | 563 +++
.../vcf/VCFStandardHeaderLinesUnitTest.java | 204 +
.../BAMCigarOverflowTest/CigarOverflowTest.bam | Bin
.../samtools/BAMFileIndexTest/index_test.bam | Bin
.../samtools/BAMFileIndexTest/index_test.bam.bai | Bin
.../BAMFileIndexTest/symlink_with_index.bam | 0
.../BAMFileIndexTest/symlink_with_index.bam.bai | 0
.../symlink_without_linked_index.bam | 0
.../SAMIntegerTagTest/variousAttributes.bam | Bin
.../SAMIntegerTagTest/variousAttributes.sam | 0
.../SamFileHeaderMergerTest/Chromosome1to10.bam | Bin
.../SamFileHeaderMergerTest/Chromosome5to9.bam | Bin
.../case1/chr11sub_file1.sam | 0
.../case1/chr11sub_file2.sam | 0
.../case1/expected_output.sam | 0
.../case2/chr11sub_file1.sam | 0
.../case2/chr11sub_file2.sam | 0
.../case2/chr11sub_file3.sam | 0
.../case2/chr11sub_file4.sam | 0
.../case2/expected_output.sam | 0
.../SamFileHeaderMergerTest/unsorted_input/1.sam | 0
.../SamFileHeaderMergerTest/unsorted_input/2.sam | 0
.../reference_with_lower_and_uppercase.dict | 3 +
.../reference_with_lower_and_uppercase.fasta | 4 +
.../reference_with_lower_and_uppercase.fasta.fai | 2 +
.../SequenceUtil/upper_and_lowercase_read.sam | 10 +
.../samtools/ValidateSamFileTest/bad_index.bai | Bin
.../samtools/ValidateSamFileTest/bad_index.bam | Bin
.../samtools/ValidateSamFileTest/buggyHeader.sam | 0
.../samtools/ValidateSamFileTest/duplicate_rg.sam | 0
.../ValidateSamFileTest/duplicated_reads.sam | 0
.../duplicated_reads_out_of_order.sam | 0
.../samtools/ValidateSamFileTest/hanging_tab.sam | 0
.../inappropriate_mate_cigar_string.sam | 0
.../invalid_coord_sort_order.sam | 0
.../invalid_mate_cigar_string.sam | 0
.../ValidateSamFileTest/invalid_platform_unit.sam | 0
.../invalid_queryname_sort_order.sam | 0
.../ValidateSamFileTest/mate_cigar_and_no_oqs.sam | 0
.../ValidateSamFileTest/mate_cigar_and_oqs.sam | 0
.../ValidateSamFileTest/missing_fields.sam | 0
.../ValidateSamFileTest/missing_platform_unit.sam | 0
.../test_samfile_version_1pt5.bam | Bin
.../samtools/ValidateSamFileTest/truncated.bam | Bin
.../ValidateSamFileTest/truncated_quals.sam | 0
.../samtools/ValidateSamFileTest/truncated_tag.sam | 0
.../htsjdk/samtools/ValidateSamFileTest/valid.sam | 0
.../ValidateSamFileTest/zero_length_read.sam | 0
.../htsjdk/samtools/block_compressed.sam.gz | Bin
.../test/resources}/htsjdk/samtools/compressed.bam | Bin
.../resources}/htsjdk/samtools/compressed.sam.gz | Bin
.../htsjdk/samtools/coordinate_sorted.sam | 0
.../cram/CRAMException/testContigNotInRef.cram | Bin
.../cram/CRAMException/testContigNotInRef.cram.bai | Bin
.../cram/CRAMException/testContigNotInRef.dict | 0
.../cram/CRAMException/testContigNotInRef.fa | 0
.../cram/CRAMException/testContigNotInRef.fa.fai | 0
.../cram/CRAMException/testContigNotInRef.fasta | 0
...78.20.21.1-100.100-SeqsPerSlice.0-unMapped.cram | Bin 0 -> 47259 bytes
....21.1-100.100-SeqsPerSlice.0-unMapped.cram.crai | Bin 0 -> 81 bytes
...78.20.21.1-100.100-SeqsPerSlice.1-unMapped.cram | Bin 0 -> 47796 bytes
....21.1-100.100-SeqsPerSlice.1-unMapped.cram.crai | Bin 0 -> 94 bytes
....20.21.1-100.100-SeqsPerSlice.500-unMapped.cram | Bin 0 -> 77664 bytes
...1.1-100.100-SeqsPerSlice.500-unMapped.cram.crai | Bin 0 -> 124 bytes
.../htsjdk/samtools/cram/auxf#values.2.1.cram | Bin
.../htsjdk/samtools/cram/auxf#values.3.0.cram | Bin
.../htsjdk/samtools/cram/auxf#values.sam | 0
.../htsjdk/samtools/cram/auxf.alteredForMD5test.fa | 2 +
.../samtools/cram/auxf.alteredForMD5test.fa.fai | 1 +
.../test/resources}/htsjdk/samtools/cram/auxf.fa | 0
.../resources}/htsjdk/samtools/cram/auxf.fa.fai | 0
.../htsjdk/samtools/cram/c1#bounds.2.1.cram | Bin
.../htsjdk/samtools/cram/c1#bounds.3.0.cram | Bin
.../resources}/htsjdk/samtools/cram/c1#bounds.sam | 0
.../htsjdk/samtools/cram/c1#clip.2.1.cram | Bin
.../htsjdk/samtools/cram/c1#clip.3.0.cram | Bin
.../resources}/htsjdk/samtools/cram/c1#clip.sam | 0
.../htsjdk/samtools/cram/c1#noseq.2.1.cram | Bin
.../htsjdk/samtools/cram/c1#noseq.3.0.cram | Bin
.../resources}/htsjdk/samtools/cram/c1#noseq.sam | 0
.../htsjdk/samtools/cram/c1#pad1.2.1.cram | Bin
.../htsjdk/samtools/cram/c1#pad1.3.0.cram | Bin
.../resources}/htsjdk/samtools/cram/c1#pad1.sam | 0
.../htsjdk/samtools/cram/c1#pad2.2.1.cram | Bin
.../htsjdk/samtools/cram/c1#pad2.3.0.cram | Bin
.../resources}/htsjdk/samtools/cram/c1#pad2.sam | 0
.../htsjdk/samtools/cram/c1#pad3.2.1.cram | Bin
.../htsjdk/samtools/cram/c1#pad3.3.0.cram | Bin
.../resources}/htsjdk/samtools/cram/c1#pad3.sam | 0
.../htsjdk/samtools/cram/c1#unknown.2.1.cram | Bin
.../htsjdk/samtools/cram/c1#unknown.3.0.cram | Bin
.../resources}/htsjdk/samtools/cram/c1#unknown.sam | 0
.../test/resources}/htsjdk/samtools/cram/c1.fa | 0
.../test/resources}/htsjdk/samtools/cram/c1.fa.fai | 0
.../htsjdk/samtools/cram/c2#pad.2.1.cram | Bin
.../htsjdk/samtools/cram/c2#pad.3.0.cram | Bin
.../resources}/htsjdk/samtools/cram/ce#1.2.1.cram | Bin
.../resources}/htsjdk/samtools/cram/ce#1.3.0.cram | Bin
.../test/resources}/htsjdk/samtools/cram/ce#1.sam | 0
.../resources}/htsjdk/samtools/cram/ce#2.2.1.cram | Bin
.../resources}/htsjdk/samtools/cram/ce#2.3.0.cram | Bin
.../test/resources}/htsjdk/samtools/cram/ce#2.sam | 0
.../resources}/htsjdk/samtools/cram/ce#5.2.1.cram | Bin
.../resources}/htsjdk/samtools/cram/ce#5.3.0.cram | Bin
.../test/resources}/htsjdk/samtools/cram/ce#5.sam | 0
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create mode 100644 src/main/java/htsjdk/samtools/BAMIndexMetaData.java
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create mode 100644 src/main/java/htsjdk/samtools/BAMIteratorFilter.java
create mode 100644 src/main/java/htsjdk/samtools/BAMQueryMultipleIntervalsIteratorFilter.java
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create mode 100644 src/main/java/htsjdk/samtools/CRAMContainerStreamWriter.java
create mode 100644 src/main/java/htsjdk/samtools/CRAMFileReader.java
create mode 100644 src/main/java/htsjdk/samtools/CRAMFileWriter.java
create mode 100644 src/main/java/htsjdk/samtools/CRAMIterator.java
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create mode 100644 src/main/java/htsjdk/samtools/SAMRecordUtil.java
create mode 100644 src/main/java/htsjdk/samtools/SAMSequenceDictionary.java
create mode 100644 src/main/java/htsjdk/samtools/SAMSequenceDictionaryCodec.java
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create mode 100644 src/main/java/htsjdk/samtools/SamFiles.java
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create mode 100644 src/main/java/htsjdk/samtools/SamInputResource.java
create mode 100644 src/main/java/htsjdk/samtools/SamPairUtil.java
create mode 100644 src/main/java/htsjdk/samtools/SamReader.java
create mode 100644 src/main/java/htsjdk/samtools/SamReaderFactory.java
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create mode 100644 src/main/java/htsjdk/samtools/cram/CRAIEntry.java
create mode 100644 src/main/java/htsjdk/samtools/cram/CRAIIndex.java
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create mode 100644 src/main/java/htsjdk/samtools/cram/build/CramNormalizer.java
rename src/{ => main}/java/htsjdk/samtools/cram/build/CramSpanContainerIterator.java (100%)
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create mode 100644 src/main/java/htsjdk/samtools/cram/build/Utils.java
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create mode 100644 src/main/java/htsjdk/samtools/cram/common/CramVersions.java
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rename src/{ => main}/java/htsjdk/samtools/cram/encoding/AbstractBitCodec.java (100%)
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rename src/{ => main}/java/htsjdk/samtools/cram/encoding/huffman/HuffmanCode.java (100%)
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rename src/{ => main}/java/htsjdk/samtools/cram/encoding/huffman/codec/HuffmanBitCode.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/encoding/huffman/codec/HuffmanByteEncoding.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/encoding/huffman/codec/HuffmanByteHelper.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/encoding/huffman/codec/HuffmanIntHelper.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/encoding/huffman/codec/HuffmanIntegerEncoding.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/encoding/huffman/codec/HuffmanParamsCalculator.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/encoding/rans/Constants.java (100%)
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rename src/{ => main}/java/htsjdk/samtools/cram/encoding/rans/Decoding.java (100%)
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rename src/{ => main}/java/htsjdk/samtools/cram/encoding/rans/Encoding.java (100%)
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rename src/{ => main}/java/htsjdk/samtools/cram/encoding/rans/RANS.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/encoding/rans/Utils.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/encoding/reader/AbstractReader.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/encoding/reader/CramRecordReader.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/encoding/reader/DataReader.java (100%)
create mode 100644 src/main/java/htsjdk/samtools/cram/encoding/reader/DataReaderFactory.java
rename src/{ => main}/java/htsjdk/samtools/cram/encoding/reader/RefSeqIdReader.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/encoding/readfeatures/BaseQualityScore.java (100%)
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rename src/{ => main}/java/htsjdk/samtools/cram/encoding/readfeatures/Deletion.java (100%)
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rename src/{ => main}/java/htsjdk/samtools/cram/encoding/readfeatures/InsertBase.java (100%)
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rename src/{ => main}/java/htsjdk/samtools/cram/encoding/readfeatures/RefSkip.java (100%)
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rename src/{ => main}/java/htsjdk/samtools/cram/encoding/readfeatures/SoftClip.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/encoding/readfeatures/Substitution.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/encoding/writer/DataWriter.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/encoding/writer/DataWriterFactory.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/encoding/writer/Writer.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/io/BitInputStream.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/io/BitOutputStream.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/io/CRC32InputStream.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/io/CRC32OutputStream.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/io/CountingInputStream.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/io/CramArray.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/io/CramInt.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/io/DefaultBitInputStream.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/io/DefaultBitOutputStream.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/io/ExposedByteArrayOutputStream.java (100%)
create mode 100644 src/main/java/htsjdk/samtools/cram/io/ExternalCompression.java
rename src/{ => main}/java/htsjdk/samtools/cram/io/ITF8.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/io/InputStreamUtils.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/io/LTF8.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/lossy/BaseCategory.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/lossy/BaseCategoryType.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/lossy/Binning.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/lossy/PreservationPolicy.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/lossy/QualityScorePreservation.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/lossy/QualityScoreTreatment.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/lossy/QualityScoreTreatmentType.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/lossy/ReadCategory.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/lossy/ReadCategoryType.java (100%)
create mode 100644 src/main/java/htsjdk/samtools/cram/ref/CRAMReferenceSource.java
rename src/{ => main}/java/htsjdk/samtools/cram/ref/EnaRefService.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/ref/InMemoryReferenceSequenceFile.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/ref/ReferenceRegion.java (100%)
create mode 100644 src/main/java/htsjdk/samtools/cram/ref/ReferenceSource.java
rename src/{ => main}/java/htsjdk/samtools/cram/ref/ReferenceTracks.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/structure/AlignmentSpan.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/structure/Block.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/structure/BlockCompressionMethod.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/structure/BlockContentType.java (100%)
create mode 100644 src/main/java/htsjdk/samtools/cram/structure/CompressionHeader.java
rename src/{ => main}/java/htsjdk/samtools/cram/structure/Container.java (100%)
create mode 100644 src/main/java/htsjdk/samtools/cram/structure/ContainerHeaderIO.java
rename src/{ => main}/java/htsjdk/samtools/cram/structure/ContainerIO.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/structure/CramCompressionRecord.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/structure/CramHeader.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/structure/EncodingID.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/structure/EncodingKey.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/structure/EncodingParams.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/structure/ReadTag.java (100%)
create mode 100644 src/main/java/htsjdk/samtools/cram/structure/Slice.java
rename src/{ => main}/java/htsjdk/samtools/cram/structure/SliceIO.java (100%)
rename src/{ => main}/java/htsjdk/samtools/cram/structure/SubstitutionMatrix.java (100%)
rename src/{ => main}/java/htsjdk/samtools/example/ExampleSamUsage.java (100%)
create mode 100755 src/main/java/htsjdk/samtools/example/PrintReadsExample.java
rename src/{ => main}/java/htsjdk/samtools/fastq/AsyncFastqWriter.java (100%)
rename src/{ => main}/java/htsjdk/samtools/fastq/BasicFastqWriter.java (100%)
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