[med-svn] [htsjdk] branch master updated (a456695 -> 2606dd7)

Andreas Tille tille at debian.org
Wed Jun 29 12:18:41 UTC 2016


This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch master
in repository htsjdk.

      from  a456695   Skip tests checking the use of the local zip implementation
       new  c9883b4   Imported Upstream version 2.5.0
       new  23d85cb   Merge tag 'upstream/2.5.0'
       new  17e0b6f   Simplified watch file, new upstream version
       new  5fdb340   Imported Upstream version 2.5.0+dfsg
       new  843f684   Merge tag 'upstream/2.5.0+dfsg'
       new  5e2962b   Build system changed to gradle - patch does not apply any more
       new  a10cf9a   Addapt patches
       new  f102f23   Try to adapt gradle build system by removing plugins we can not download
       new  e143bf7   Try to rework the patch for gradle (but failed :-()
       new  2606dd7   Upstream has changed build system to gradle

The 10 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                                          |   67 +-
 build.gradle                                       |  226 +
 build.sbt                                          |  154 -
 build.xml                                          |  281 +-
 debian/changelog                                   |    3 +-
 debian/control                                     |    3 +-
 debian/patches/10-build.xml                        |   66 -
 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               |   47 +-
 debian/patches/14-skip_local_zlib_tests            |   28 -
 debian/patches/series                              |    4 +-
 debian/rules                                       |    2 +-
 debian/watch                                       |    2 +-
 etc/test/junit-noframes.xsl                        |  581 ---
 etc/test/testng.css                                |   26 -
 gradle/wrapper/gradle-wrapper.jar                  |  Bin 0 -> 53556 bytes
 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                |  392 --
 src/c/inteldeflater/README                         |    7 -
 src/c/inteldeflater/igzip_lib.h                    |   50 -
 src/c/inteldeflater/internal_state_size.h          |   32 -
 src/c/inteldeflater/types.h                        |   46 -
 src/java/htsjdk/samtools/BAMFileReader.java        |  989 ----
 src/java/htsjdk/samtools/BAMFileWriter.java        |  193 -
 src/java/htsjdk/samtools/CRAMFileReader.java       |  625 ---
 src/java/htsjdk/samtools/CRAMIterator.java         |  306 --
 src/java/htsjdk/samtools/Defaults.java             |  186 -
 src/java/htsjdk/samtools/SAMFileReader.java        |  751 ---
 src/java/htsjdk/samtools/SAMFileWriterFactory.java |  465 --
 src/java/htsjdk/samtools/SAMFlag.java              |  110 -
 src/java/htsjdk/samtools/SAMLineParser.java        |  469 --
 src/java/htsjdk/samtools/SAMRecordSetBuilder.java  |  577 ---
 src/java/htsjdk/samtools/SAMTextWriter.java        |  188 -
 src/java/htsjdk/samtools/SRAFileReader.java        |  306 --
 src/java/htsjdk/samtools/SRAIterator.java          |  248 -
 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/SamReaderFactory.java     |  507 --
 src/java/htsjdk/samtools/SamStreams.java           |   99 -
 src/java/htsjdk/samtools/cram/CRAIEntry.java       |  177 -
 src/java/htsjdk/samtools/cram/CRAIIndex.java       |  161 -
 .../htsjdk/samtools/cram/common/CramVersions.java  |   11 -
 .../samtools/cram/io/ExternalCompression.java      |  151 -
 .../htsjdk/samtools/cram/ref/ReferenceSource.java  |  274 --
 .../samtools/cram/structure/ContainerHeaderIO.java |   88 -
 .../htsjdk/samtools/example/PrintReadsExample.java |  104 -
 .../htsjdk/samtools/fastq/FastqWriterFactory.java  |   31 -
 src/java/htsjdk/samtools/liftover/LiftOver.java    |  292 --
 src/java/htsjdk/samtools/metrics/MetricsFile.java  |  592 ---
 .../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 -
 .../samtools/util/BlockCompressedOutputStream.java |  336 --
 src/java/htsjdk/samtools/util/Histogram.java       |  480 --
 src/java/htsjdk/samtools/util/Objects.java         |   12 -
 src/java/htsjdk/samtools/util/OverlapDetector.java |  126 -
 .../htsjdk/samtools/util/SamLocusIterator.java     |  552 ---
 .../htsjdk/samtools/util/SortingCollection.java    |  532 ---
 .../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/AsciiFeatureCodec.java     |   97 -
 src/java/htsjdk/tribble/TabixFeatureReader.java    |  221 -
 .../tribble/readers/AsynchronousLineReader.java    |   98 -
 .../htsjdk/tribble/readers/LineReaderUtil.java     |   94 -
 src/java/htsjdk/variant/bcf2/BCF2Codec.java        |  494 --
 .../variant/example/PrintVariantsExample.java      |  105 -
 .../variantcontext/VariantContextBuilder.java      |  500 --
 .../writer/VariantContextWriterBuilder.java        |  525 --
 .../writer/VariantContextWriterFactory.java        |  282 --
 .../variant/vcf/VCFHeaderLineTranslator.java       |  157 -
 .../java/htsjdk/samtools/AbstractBAMFileIndex.java |    0
 .../htsjdk/samtools/AbstractSAMHeaderRecord.java   |    0
 .../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     |    0
 .../java/htsjdk/samtools/BAMIndexWriter.java       |    0
 .../java/htsjdk/samtools/BAMIndexer.java           |    0
 .../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  |    0
 .../java/htsjdk/samtools/BinningIndexContent.java  |    0
 .../java/htsjdk/samtools/BrowseableBAMIndex.java   |    0
 .../java/htsjdk/samtools/CRAMBAIIndexer.java       |    0
 src/main/java/htsjdk/samtools/CRAMCRAIIndexer.java |  135 +
 .../htsjdk/samtools/CRAMContainerStreamWriter.java |    0
 src/main/java/htsjdk/samtools/CRAMFileReader.java  |  533 +++
 .../java/htsjdk/samtools/CRAMFileWriter.java       |    0
 src/main/java/htsjdk/samtools/CRAMIterator.java    |  306 ++
 .../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   |    0
 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  |    0
 .../java/htsjdk/samtools/DuplicateSet.java         |    0
 .../java/htsjdk/samtools/DuplicateSetIterator.java |    0
 .../htsjdk/samtools/FileTruncatedException.java    |    0
 .../java/htsjdk/samtools/FixBAMFile.java           |    0
 .../java/htsjdk/samtools/GenomicIndexUtil.java     |    0
 .../samtools/HighAccuracyDownsamplingIterator.java |    0
 .../java/htsjdk/samtools/LinearIndex.java          |    0
 .../htsjdk/samtools/MergingSamRecordIterator.java  |    0
 .../samtools/NotPrimarySkippingIterator.java       |    0
 .../java/htsjdk/samtools/QueryInterval.java        |    0
 .../java/htsjdk/samtools/ReservedTagConstants.java |    0
 .../SAMBinaryTagAndUnsignedArrayValue.java         |    0
 .../java/htsjdk/samtools/SAMBinaryTagAndValue.java |    0
 .../java/htsjdk/samtools/SAMException.java         |    0
 .../java/htsjdk/samtools/SAMFileHeader.java        |    0
 src/main/java/htsjdk/samtools/SAMFileReader.java   |  751 +++
 .../java/htsjdk/samtools/SAMFileSource.java        |    0
 .../java/htsjdk/samtools/SAMFileSpan.java          |    0
 .../htsjdk/samtools/SAMFileTruncatedReader.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 |    0
 .../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 +++
 .../java/htsjdk/samtools/SAMRecordUtil.java        |    0
 .../htsjdk/samtools/SAMSequenceDictionary.java     |    0
 .../java/htsjdk/samtools/SAMSequenceRecord.java    |    0
 .../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   |    0
 .../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  |    0
 .../java/htsjdk/samtools/SAMValidationError.java   |    0
 src/{ => main}/java/htsjdk/samtools/SQTagUtil.java |    0
 src/main/java/htsjdk/samtools/SRAFileReader.java   |  308 ++
 src/{ => main}/java/htsjdk/samtools/SRAIndex.java  |    0
 src/main/java/htsjdk/samtools/SRAIterator.java     |  256 +
 .../java/htsjdk/samtools/SamFileHeaderMerger.java  |    0
 .../java/htsjdk/samtools/SamFileValidator.java     |  856 ++++
 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     |  473 ++
 .../java/htsjdk/samtools/SamPairUtil.java          |    0
 src/{ => main}/java/htsjdk/samtools/SamReader.java |    0
 .../java/htsjdk/samtools/SamReaderFactory.java     |  528 +++
 src/main/java/htsjdk/samtools/SamStreams.java      |  164 +
 .../SecondaryOrSupplementarySkippingIterator.java  |    0
 .../StreamInflatingIndexingOutputStream.java       |    0
 .../samtools/TagValueAndUnsignedArrayFlag.java     |    0
 .../java/htsjdk/samtools/TextCigarCodec.java       |    0
 .../java/htsjdk/samtools/TextTagCodec.java         |    0
 .../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 |    0
 .../cram/build/CramSpanContainerIterator.java      |    0
 .../samtools/cram/build/Sam2CramRecordFactory.java |    0
 .../java/htsjdk/samtools/cram/build/Utils.java     |    0
 .../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    |    0
 .../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     |    0
 .../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  |  274 ++
 .../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 |    0
 .../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 |    0
 .../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  |    0
 .../samtools/filter/FilteringSamIterator.java      |    0
 .../htsjdk/samtools/filter/InsertSizeFilter.java   |    0
 .../htsjdk/samtools/filter/IntervalFilter.java     |    0
 .../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      |    0
 .../samtools/reference/ReferenceSequenceFile.java  |    0
 .../reference/ReferenceSequenceFileFactory.java    |    0
 .../reference/ReferenceSequenceFileWalker.java     |    0
 .../seekablestream/ByteArraySeekableStream.java    |    0
 .../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     |  174 +
 .../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  |    0
 .../htsjdk/samtools/util/AbstractIterator.java     |    0
 .../samtools/util/AbstractProgressLogger.java      |    0
 .../java/htsjdk/samtools/util/AsciiWriter.java     |    0
 .../samtools/util/AsyncBufferedIterator.java       |    0
 .../java/htsjdk/samtools/util/BinaryCodec.java     |    0
 .../util/BlockCompressedFilePointerUtil.java       |    0
 .../samtools/util/BlockCompressedInputStream.java  |    0
 .../samtools/util/BlockCompressedOutputStream.java |  392 ++
 .../util/BlockCompressedStreamConstants.java       |    0
 .../java/htsjdk/samtools/util/BlockGunzipper.java  |    0
 .../htsjdk/samtools/util/BufferedLineReader.java   |    0
 .../java/htsjdk/samtools/util/CigarUtil.java       |    0
 .../htsjdk/samtools/util/CloseableIterator.java    |    0
 .../java/htsjdk/samtools/util/CloserUtil.java      |    0
 .../java/htsjdk/samtools/util/CodeUtil.java        |    0
 .../java/htsjdk/samtools/util/CollectionUtil.java  |    0
 .../java/htsjdk/samtools/util/ComparableTuple.java |    0
 .../java/htsjdk/samtools/util/CoordMath.java       |    0
 .../htsjdk/samtools/util/CoordSpanInputSteam.java  |    0
 .../java/htsjdk/samtools/util/DateParser.java      |    0
 .../htsjdk/samtools/util/DelegatingIterator.java   |    0
 .../java/htsjdk/samtools/util/DiskBackedQueue.java |    0
 .../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
 .../java/htsjdk/samtools/util/IOUtil.java          |    0
 .../java/htsjdk/samtools/util/Interval.java        |    0
 .../java/htsjdk/samtools/util/IntervalList.java    |    0
 .../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 |    0
 .../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  |    0
 .../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
 .../java/htsjdk/samtools/util/ProcessExecutor.java |    0
 .../java/htsjdk/samtools/util/ProgressLogger.java  |    0
 .../samtools/util/ProgressLoggerInterface.java     |    0
 .../samtools/util/QualityEncodingDetector.java     |    0
 .../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     |  679 +++
 .../util/SamRecordIntervalIteratorFactory.java     |    0
 .../samtools/util/SamRecordTrackingBuffer.java     |    0
 .../htsjdk/samtools/util/SamRecordWithOrdinal.java |    0
 .../java/htsjdk/samtools/util/SequenceUtil.java    |    0
 .../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
 .../java/htsjdk/samtools/util/StringUtil.java      |    0
 .../htsjdk/samtools/util/TempStreamFactory.java    |    0
 .../java/htsjdk/samtools/util/TestUtil.java        |    0
 .../java/htsjdk/samtools/util/TrimmingUtil.java    |    0
 .../java/htsjdk/samtools/util/Tuple.java           |    0
 .../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 |    0
 .../java/htsjdk/tribble/AsciiFeatureCodec.java     |   92 +
 .../java/htsjdk/tribble/BinaryFeatureCodec.java    |    0
 .../htsjdk/tribble/CloseableTribbleIterator.java   |    0
 src/{ => main}/java/htsjdk/tribble/Feature.java    |    0
 .../java/htsjdk/tribble/FeatureCodec.java          |    0
 .../java/htsjdk/tribble/FeatureCodecHeader.java    |    0
 .../java/htsjdk/tribble/FeatureReader.java         |    0
 .../java/htsjdk/tribble/NameAwareCodec.java        |    0
 .../java/htsjdk/tribble/SimpleFeature.java         |    0
 .../java/htsjdk/tribble/TabixFeatureReader.java    |  217 +
 src/{ => main}/java/htsjdk/tribble/Tribble.java    |    0
 .../java/htsjdk/tribble/TribbleException.java      |    0
 .../tribble/TribbleIndexedFeatureReader.java       |    0
 .../java/htsjdk/tribble/annotation/Strand.java     |    0
 .../java/htsjdk/tribble/bed/BEDCodec.java          |    0
 .../java/htsjdk/tribble/bed/BEDFeature.java        |    0
 .../java/htsjdk/tribble/bed/FullBEDFeature.java    |    0
 .../java/htsjdk/tribble/bed/SimpleBEDFeature.java  |    0
 .../java/htsjdk/tribble/example/CountRecords.java  |    0
 .../htsjdk/tribble/example/ExampleBinaryCodec.java |    0
 .../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   |    0
 .../java/htsjdk/tribble/index/AbstractIndex.java   |    0
 .../java/htsjdk/tribble/index/Block.java           |    0
 .../java/htsjdk/tribble/index/ChrIndex.java        |    0
 .../htsjdk/tribble/index/DynamicIndexCreator.java  |    0
 .../java/htsjdk/tribble/index/Index.java           |    0
 .../java/htsjdk/tribble/index/IndexCreator.java    |    0
 .../java/htsjdk/tribble/index/IndexFactory.java    |    0
 .../java/htsjdk/tribble/index/MutableIndex.java    |    0
 .../htsjdk/tribble/index/TribbleIndexCreator.java  |    0
 .../htsjdk/tribble/index/interval/Interval.java    |    0
 .../index/interval/IntervalIndexCreator.java       |    0
 .../tribble/index/interval/IntervalTree.java       |    0
 .../tribble/index/interval/IntervalTreeIndex.java  |    0
 .../htsjdk/tribble/index/linear/LinearIndex.java   |    0
 .../tribble/index/linear/LinearIndexCreator.java   |    0
 .../htsjdk/tribble/index/tabix/TabixFormat.java    |    0
 .../htsjdk/tribble/index/tabix/TabixIndex.java     |    0
 .../tribble/index/tabix/TabixIndexCreator.java     |    0
 .../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  |    0
 .../variant/variantcontext/FastGenotype.java       |    0
 .../htsjdk/variant/variantcontext/Genotype.java    |    0
 .../variant/variantcontext/GenotypeBuilder.java    |    0
 .../variantcontext/GenotypeJEXLContext.java        |    0
 .../variantcontext/GenotypeLikelihoods.java        |    0
 .../variant/variantcontext/GenotypeType.java       |    0
 .../variant/variantcontext/GenotypesContext.java   |    0
 .../htsjdk/variant/variantcontext/JEXLMap.java     |    0
 .../variantcontext/LazyGenotypesContext.java       |    0
 .../variant/variantcontext/VariantContext.java     |    0
 .../variantcontext/VariantContextBuilder.java      |  498 ++
 .../variantcontext/VariantContextComparator.java   |    0
 .../variantcontext/VariantContextUtils.java        |    0
 .../variant/variantcontext/VariantJEXLContext.java |    0
 .../variantcontext/filter/CompoundFilter.java      |    0
 .../variantcontext/filter/FilteringIterator.java   |    0
 .../filter/FilteringVariantContextIterator.java    |    0
 .../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     |    0
 .../writer/BCF2FieldWriterManager.java             |    0
 .../variant/variantcontext/writer/BCF2Writer.java  |    0
 .../writer/IndexingVariantContextWriter.java       |    0
 .../writer/IntGenotypeFieldAccessors.java          |    0
 .../variant/variantcontext/writer/Options.java     |    0
 .../writer/SortingVariantContextWriter.java        |    0
 .../writer/SortingVariantContextWriterBase.java    |    0
 .../variant/variantcontext/writer/VCFWriter.java   |    0
 .../writer/VariantContextWriter.java               |    0
 .../writer/VariantContextWriterBuilder.java        |  537 +++
 .../writer/VariantContextWriterFactory.java        |  282 ++
 .../java/htsjdk/variant/vcf/AbstractVCFCodec.java  |    0
 .../java/htsjdk/variant/vcf/VCF3Codec.java         |    0
 .../java/htsjdk/variant/vcf/VCFCodec.java          |    0
 .../htsjdk/variant/vcf/VCFCompoundHeaderLine.java  |    0
 .../java/htsjdk/variant/vcf/VCFConstants.java      |    0
 .../htsjdk/variant/vcf/VCFContigHeaderLine.java    |    0
 .../java/htsjdk/variant/vcf/VCFEncoder.java        |    0
 .../java/htsjdk/variant/vcf/VCFFileReader.java     |    0
 .../htsjdk/variant/vcf/VCFFilterHeaderLine.java    |    0
 .../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 |    0
 .../java/htsjdk/variant/vcf/VCFUtils.java          |    0
 src/scripts/build_intel_deflater.sh                |   78 -
 .../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    |    0
 .../java/htsjdk/samtools/BAMIndexWriterTest.java   |  227 +
 src/test/java/htsjdk/samtools/BAMIteratorTest.java |   71 +
 ...AMQueryMultipleIntervalsIteratorFilterTest.java |  146 +
 .../java/htsjdk/samtools/BAMRemoteFileTest.java    |  326 ++
 .../java/htsjdk/samtools/BinTest.java              |    0
 .../java/htsjdk/samtools/CRAMBAIIndexerTest.java   |    0
 .../java/htsjdk/samtools/CRAMCRAIIndexerTest.java  |  178 +
 .../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   |  163 +
 .../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 |    0
 ...MergingSamRecordIteratorGroupCollisionTest.java |    0
 .../samtools/MergingSamRecordIteratorTest.java     |    0
 .../htsjdk/samtools/ProgramRecordChainingTest.java |    0
 .../samtools/SAMBinaryTagAndValueUnitTest.java     |    0
 .../java/htsjdk/samtools/SAMCloneTest.java         |    0
 .../java/htsjdk/samtools/SAMFileReaderTest.java    |  170 +
 .../htsjdk/samtools/SAMFileWriterFactoryTest.java  |  307 ++
 .../java/htsjdk/samtools/SAMFlagTest.java          |    0
 .../java/htsjdk/samtools/SAMIntegerTagTest.java    |  329 ++
 .../samtools/SAMRecordDuplicateComparatorTest.java |    0
 .../java/htsjdk/samtools/SAMRecordUnitTest.java    |  963 ++++
 .../htsjdk/samtools/SAMSequenceDictionaryTest.java |    0
 .../java/htsjdk/samtools/SAMTextReaderTest.java    |    0
 .../java/htsjdk/samtools/SAMTextWriterTest.java    |  130 +
 .../java/htsjdk/samtools/SAMUtilsTest.java         |    0
 .../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 |  437 ++
 .../java/htsjdk/samtools/SamReaderSortTest.java    |  102 +
 src/test/java/htsjdk/samtools/SamSpecIntTest.java  |   97 +
 src/test/java/htsjdk/samtools/SamStreamsTest.java  |  124 +
 .../SequenceNameTruncationAndValidationTest.java   |   98 +
 .../java/htsjdk/samtools/ValidateSamFileTest.java  |  471 ++
 .../java/htsjdk/samtools/apps/.gitignore           |    0
 .../java/htsjdk/samtools/cram/CRAIEntryTest.java   |    0
 .../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 |    0
 .../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/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  |   44 +
 .../java/htsjdk/samtools/sra/AbstractSRATest.java  |    0
 .../java/htsjdk/samtools/sra/SRAAccessionTest.java |   29 +
 .../java/htsjdk/samtools/sra/SRAIndexTest.java     |    0
 .../htsjdk/samtools/sra/SRALazyRecordTest.java     |    0
 .../java/htsjdk/samtools/sra/SRAQueryTest.java     |    0
 .../java/htsjdk/samtools/sra/SRAReferenceTest.java |   95 +
 src/test/java/htsjdk/samtools/sra/SRATest.java     |  432 ++
 .../samtools/util/AsyncBufferedIteratorTest.java   |    0
 .../java/htsjdk/samtools/util/BinaryCodecTest.java |    0
 .../util/BlockCompressedFilePointerUtilTest.java   |    0
 .../util/BlockCompressedOutputStreamTest.java      |  165 +
 .../util/BlockCompressedTerminatorTest.java        |   59 +
 .../java/htsjdk/samtools/util/CigarUtilTest.java   |    0
 .../samtools/util/CloseableIteratorTest.java       |    0
 .../java/htsjdk/samtools/util/CodeUtilTest.java    |    0
 .../htsjdk/samtools/util/ComparableTupleTest.java  |    0
 .../samtools/util/CoordSpanInputSteamTest.java     |    0
 .../htsjdk/samtools/util/DiskBackedQueueTest.java  |    0
 .../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/QualityEncodingDetectorTest.java |  109 +
 .../samtools/util/RelativeIso8601DateTest.java     |    0
 .../htsjdk/samtools/util/SamLocusIteratorTest.java |  676 +++
 .../htsjdk/samtools/util/SequenceUtilTest.java     |    0
 .../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  |    0
 .../htsjdk/samtools/util/TrimmingUtilTest.java     |    0
 .../java/htsjdk/samtools/util/TupleTest.java       |    0
 .../htsjdk/tribble/AbstractFeatureReaderTest.java  |    0
 .../java/htsjdk/tribble/BinaryFeaturesTest.java    |    0
 .../java/htsjdk/tribble/FeatureReaderTest.java     |    0
 src/test/java/htsjdk/tribble/TestUtils.java        |   28 +
 .../tribble/TribbleIndexFeatureReaderTest.java     |    0
 .../java/htsjdk/tribble/TribbleTest.java           |    0
 .../java/htsjdk/tribble/bed/BEDCodecTest.java      |    0
 .../java/htsjdk/tribble/gelitext/GeliTextTest.java |    0
 .../htsjdk/tribble/index/IndexFactoryTest.java     |  115 +
 .../java/htsjdk/tribble/index/IndexTest.java       |    0
 .../tribble/index/interval/IntervalTreeTest.java   |    0
 .../tribble/index/linear/LinearIndexTest.java      |    0
 .../htsjdk/tribble/index/tabix/TabixIndexTest.java |  143 +
 .../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    |    0
 .../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
 .../GenotypeLikelihoodsUnitTest.java               |  337 ++
 .../variant/variantcontext/GenotypeUnitTest.java   |    0
 .../variantcontext/GenotypesContextUnitTest.java   |    0
 .../variantcontext/VariantContextBuilderTest.java  |    0
 .../variantcontext/VariantContextTestProvider.java | 1014 ++++
 .../variantcontext/VariantContextUnitTest.java     | 1450 ++++++
 .../variantcontext/VariantJEXLContextUnitTest.java |    0
 .../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           |    0
 .../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   |   53 +
 .../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 |  561 +++
 .../vcf/VCFStandardHeaderLinesUnitTest.java        |    0
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 .../cram/human_g1k_v37.20.21.10M-10M200k.fasta     | 5002 ++++++++++++++++++++
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 .../samtools/util/QualityEncodingDetectorTest.java |  109 -
 .../htsjdk/samtools/util/SamLocusIteratorTest.java |  231 -
 src/tests/java/htsjdk/tribble/TestUtils.java       |   28 -
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 .../java/htsjdk/variant/vcf/VCFHeaderUnitTest.java |  491 --
 1398 files changed, 39868 insertions(+), 32832 deletions(-)
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