[med-svn] [htsjdk] branch upstream updated (ad6800c -> a6a2d54)
Vincent Danjean
vdanjean at debian.org
Mon Mar 14 20:11:34 UTC 2016
This is an automated email from the git hooks/post-receive script.
vdanjean pushed a change to branch upstream
in repository htsjdk.
from ad6800c Imported Upstream version 2.0.1+dfsg.1
new a6a2d54 Imported Upstream version 2.1.1+dfsg.1
The 1 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:
.github/ISSUE_TEMPLATE.md | 21 +
.github/PULL_REQUEST_TEMPLATE.md | 11 +
.travis.yml | 2 +-
README.md | 2 +
build.sbt | 2 +-
build.xml | 62 +-
src/java/htsjdk/samtools/BAMFileReader.java | 2 +-
src/java/htsjdk/samtools/BAMFileWriter.java | 2 +-
src/java/htsjdk/samtools/BAMIndexMetaData.java | 4 +-
src/java/htsjdk/samtools/BamIndexValidator.java | 88 +-
...eWriter.java => CRAMContainerStreamWriter.java} | 364 ++++---
src/java/htsjdk/samtools/CRAMFileReader.java | 146 ++-
src/java/htsjdk/samtools/CRAMFileWriter.java | 427 +-------
src/java/htsjdk/samtools/CRAMIndexer.java | 130 ++-
src/java/htsjdk/samtools/CRAMIterator.java | 34 +-
src/java/htsjdk/samtools/Cigar.java | 85 +-
src/java/htsjdk/samtools/CigarElement.java | 5 +
src/java/htsjdk/samtools/CigarOperator.java | 25 +
src/java/htsjdk/samtools/Defaults.java | 4 +-
.../htsjdk/samtools/DiskBasedBAMFileIndex.java | 8 +-
src/java/htsjdk/samtools/DuplicateSetIterator.java | 16 +-
.../samtools/HighAccuracyDownsamplingIterator.java | 2 +-
.../htsjdk/samtools/MergingSamRecordIterator.java | 4 +-
src/java/htsjdk/samtools/SAMFileWriterFactory.java | 55 +-
src/java/htsjdk/samtools/SAMFileWriterImpl.java | 12 +-
.../htsjdk/samtools/SAMHeaderRecordComparator.java | 4 +-
src/java/htsjdk/samtools/SAMLineParser.java | 4 +-
src/java/htsjdk/samtools/SAMRecord.java | 243 +++--
.../samtools/SAMRecordCoordinateComparator.java | 6 +-
.../samtools/SAMRecordDuplicateComparator.java | 5 +-
.../samtools/SAMRecordQueryHashComparator.java | 8 +-
.../samtools/SAMRecordQueryNameComparator.java | 5 +-
src/java/htsjdk/samtools/SAMTextHeaderCodec.java | 2 +-
src/java/htsjdk/samtools/SAMUtils.java | 15 +-
src/java/htsjdk/samtools/SAMValidationError.java | 3 +-
src/java/htsjdk/samtools/SamFileHeaderMerger.java | 2 +-
src/java/htsjdk/samtools/SamFileValidator.java | 24 +-
src/java/htsjdk/samtools/SamFiles.java | 32 +-
src/java/htsjdk/samtools/SamReaderFactory.java | 29 +-
src/java/htsjdk/samtools/TextTagCodec.java | 12 +-
.../htsjdk/samtools/TextualBAMIndexWriter.java | 2 +-
src/java/htsjdk/samtools/cram/CRAIIndex.java | 2 +-
.../cram/build/CompressionHeaderFactory.java | 1118 ++++++++------------
.../samtools/cram/build/ContainerFactory.java | 29 +-
.../samtools/cram/build/ContainerParser.java | 81 +-
src/java/htsjdk/samtools/cram/build/CramIO.java | 24 +-
.../htsjdk/samtools/cram/build/CramNormalizer.java | 3 +
.../samtools/cram/build/Sam2CramRecordFactory.java | 2 -
.../htsjdk/samtools/cram/common/CramVersions.java | 6 +-
.../codec/CanonicalHuffmanIntegerCodec.java | 8 +-
.../huffman/codec/HuffmanParamsCalculator.java | 137 +++
.../cram/encoding/reader/DataReaderFactory.java | 24 +-
.../cram/encoding/reader/RefSeqIdReader.java | 242 +++++
.../encoding/readfeatures/BaseQualityScore.java | 6 +-
.../cram/encoding/readfeatures/InsertBase.java | 6 +-
.../cram/encoding/readfeatures/ReadBase.java | 11 +-
.../cram/encoding/readfeatures/Substitution.java | 7 +-
.../cram/lossy/QualityScorePreservation.java | 2 +-
.../htsjdk/samtools/cram/ref/ReferenceSource.java | 37 +
.../samtools/cram/structure/AlignmentSpan.java | 92 ++
.../htsjdk/samtools/cram/structure/Container.java | 12 +-
.../cram/structure/CramCompressionRecord.java | 10 +-
src/java/htsjdk/samtools/cram/structure/Slice.java | 29 +-
.../cram/structure/SubstitutionMatrix.java | 4 +-
.../htsjdk/samtools/fastq/BasicFastqWriter.java | 6 +-
src/java/htsjdk/samtools/fastq/FastqReader.java | 1 +
src/java/htsjdk/samtools/fastq/FastqRecord.java | 20 +-
.../samtools/filter/AbstractJavascriptFilter.java | 159 +++
.../samtools/filter/JavascriptSamRecordFilter.java | 101 ++
src/java/htsjdk/samtools/metrics/MetricBase.java | 4 +-
src/java/htsjdk/samtools/metrics/MetricsFile.java | 10 +-
.../reference/AbstractFastaSequenceFile.java | 2 +-
.../reference/IndexedFastaSequenceFile.java | 2 +-
src/java/htsjdk/samtools/sra/SRAAccession.java | 36 +-
.../samtools/util/AbstractProgressLogger.java | 8 +-
src/java/htsjdk/samtools/util/BinaryCodec.java | 8 +-
.../htsjdk/samtools/util/BufferedLineReader.java | 2 +-
src/java/htsjdk/samtools/util/CigarUtil.java | 4 +-
src/java/htsjdk/samtools/util/CollectionUtil.java | 59 +-
src/java/htsjdk/samtools/util/ComparableTuple.java | 28 +
src/java/htsjdk/samtools/util/DateParser.java | 30 +-
src/java/htsjdk/samtools/util/DiskBackedQueue.java | 2 +-
src/java/htsjdk/samtools/util/FormatUtil.java | 2 +-
src/java/htsjdk/samtools/util/IOUtil.java | 4 +-
src/java/htsjdk/samtools/util/IntervalList.java | 9 +-
src/java/htsjdk/samtools/util/LocusComparator.java | 4 +-
src/java/htsjdk/samtools/util/Log.java | 12 +-
src/java/htsjdk/samtools/util/Murmur3.java | 6 +-
src/java/htsjdk/samtools/util/ProcessExecutor.java | 2 +-
...FException.java => RuntimeScriptException.java} | 15 +-
.../htsjdk/samtools/util/SamLocusIterator.java | 38 +-
.../samtools/util/SamRecordTrackingBuffer.java | 6 +-
src/java/htsjdk/samtools/util/SequenceUtil.java | 157 ++-
.../htsjdk/samtools/util/SortingCollection.java | 4 +-
.../samtools/util/SortingLongCollection.java | 4 +-
src/java/htsjdk/samtools/util/StringUtil.java | 12 +-
src/java/htsjdk/samtools/util/TrimmingUtil.java | 67 ++
src/java/htsjdk/samtools/util/Tuple.java | 26 +
src/java/htsjdk/tribble/bed/BEDCodec.java | 4 +-
.../index/interval/IntervalIndexCreator.java | 8 +-
.../tribble/index/interval/IntervalTree.java | 8 +-
.../tribble/index/interval/IntervalTreeIndex.java | 2 +-
.../tribble/index/linear/LinearIndexCreator.java | 4 +-
src/java/htsjdk/tribble/readers/TabixReader.java | 4 +-
src/java/htsjdk/variant/bcf2/BCF2Codec.java | 2 +-
src/java/htsjdk/variant/bcf2/BCF2Utils.java | 4 +-
.../htsjdk/variant/variantcontext/CommonInfo.java | 4 +-
.../htsjdk/variant/variantcontext/Genotype.java | 8 +-
.../variantcontext/GenotypeLikelihoods.java | 161 ++-
.../variant/variantcontext/VariantContext.java | 39 +-
.../variantcontext/VariantContextBuilder.java | 14 +-
.../variantcontext/VariantContextComparator.java | 8 +-
.../variantcontext/VariantContextUtils.java | 62 +-
.../filter/JavascriptVariantFilter.java | 97 ++
.../variant/variantcontext/writer/BCF2Encoder.java | 2 +-
.../writer/SortingVariantContextWriterBase.java | 5 +-
src/java/htsjdk/variant/vcf/AbstractVCFCodec.java | 8 +-
src/java/htsjdk/variant/vcf/VCF3Codec.java | 2 +-
src/java/htsjdk/variant/vcf/VCFCodec.java | 2 +-
src/java/htsjdk/variant/vcf/VCFEncoder.java | 34 +-
src/java/htsjdk/variant/vcf/VCFHeaderLine.java | 20 +-
src/java/htsjdk/variant/vcf/VCFUtils.java | 2 +-
.../java/htsjdk/samtools/BAMFileWriterTest.java | 42 +-
.../java/htsjdk/samtools/CRAMBAIIndexerTest.java | 87 ++
.../java/htsjdk/samtools/CRAMComplianceTest.java | 4 +-
.../samtools/CRAMContainerStreamWriterTest.java | 184 ++++
.../java/htsjdk/samtools/CRAMFileIndexTest.java | 40 +-
.../java/htsjdk/samtools/CRAMFileReaderTest.java | 163 +++
.../samtools/CRAMFileWriterWithIndexTest.java | 6 +-
src/tests/java/htsjdk/samtools/CigarTest.java | 24 +
.../java/htsjdk/samtools/CramFileWriterTest.java | 48 +
.../java/htsjdk/samtools/SAMFileReaderTest.java | 2 +-
.../java/htsjdk/samtools/SAMRecordUnitTest.java | 162 ++-
src/tests/java/htsjdk/samtools/SAMUtilsTest.java | 37 +-
src/tests/java/htsjdk/samtools/SamFilesTest.java | 21 +
.../java/htsjdk/samtools/ValidateSamFileTest.java | 69 +-
.../samtools/cram/LosslessRoundTripTest.java | 68 ++
.../cram/build/CompressionHeaderFactoryTest.java | 208 ++++
.../samtools/cram/build/ContainerFactoryTest.java | 134 +++
.../samtools/cram/build/ContainerParserTest.java | 185 ++++
.../cram/encoding/huffman/codec/HuffmanTest.java | 18 +-
.../htsjdk/samtools/cram/structure/SliceTests.java | 36 +
.../htsjdk/samtools/fastq/FastqWriterTest.java | 73 ++
.../filter/JavascriptSamRecordFilterTest.java | 74 ++
.../java/htsjdk/samtools/sra/AbstractSRATest.java | 57 +
.../java/htsjdk/samtools/sra/SRAAccessionTest.java | 29 +
.../java/htsjdk/samtools/sra/SRAIndexTest.java | 56 +-
.../htsjdk/samtools/sra/SRALazyRecordTest.java | 12 +-
.../java/htsjdk/samtools/sra/SRAQueryTest.java | 67 +-
.../java/htsjdk/samtools/sra/SRAReferenceTest.java | 10 +-
src/tests/java/htsjdk/samtools/sra/SRATest.java | 115 +-
.../htsjdk/samtools/util/ComparableTupleTest.java | 61 ++
src/tests/java/htsjdk/samtools/util/IupacTest.java | 2 +-
.../htsjdk/samtools/util/SequenceUtilTest.java | 236 ++++-
.../htsjdk/samtools/util/TrimmingUtilTest.java | 70 ++
src/tests/java/htsjdk/samtools/util/TupleTest.java | 62 ++
.../htsjdk/tribble/util/ftp/FTPClientTest.java | 77 +-
.../GenotypeLikelihoodsUnitTest.java | 161 ++-
.../variant/variantcontext/GenotypeUnitTest.java | 2 +
.../filter/JavascriptVariantFilterTest.java | 72 ++
.../htsjdk/variant/vcf/VCFHeaderLineUnitTest.java | 43 +
.../java/htsjdk/variant/vcf/VCFHeaderUnitTest.java | 101 +-
.../BAMFileIndexTest/symlink_with_index.bam | 1 +
.../BAMFileIndexTest/symlink_with_index.bam.bai | 1 +
.../symlink_without_linked_index.bam | 1 +
.../ValidateSamFileTest/duplicated_reads.sam | 17 +
.../duplicated_reads_out_of_order.sam | 17 +
...auxf#values.2.1.cram => cram_query_sorted.cram} | Bin 11427 -> 13266 bytes
.../{cram_tlen.fasta => cram_query_sorted.fasta} | 3 +-
..._tlen.fasta.fai => cram_query_sorted.fasta.fai} | 4 +-
testdata/htsjdk/samtools/samFilter01.js | 2 +
testdata/htsjdk/samtools/samFilter02.js | 9 +
testdata/htsjdk/variant/variantFilter01.js | 2 +
testdata/htsjdk/variant/variantFilter02.js | 20 +
174 files changed, 5947 insertions(+), 2203 deletions(-)
create mode 100644 .github/ISSUE_TEMPLATE.md
create mode 100644 .github/PULL_REQUEST_TEMPLATE.md
copy src/java/htsjdk/samtools/{CRAMFileWriter.java => CRAMContainerStreamWriter.java} (75%)
create mode 100644 src/java/htsjdk/samtools/cram/encoding/huffman/codec/HuffmanParamsCalculator.java
create mode 100644 src/java/htsjdk/samtools/cram/encoding/reader/RefSeqIdReader.java
create mode 100644 src/java/htsjdk/samtools/cram/structure/AlignmentSpan.java
create mode 100644 src/java/htsjdk/samtools/filter/AbstractJavascriptFilter.java
create mode 100644 src/java/htsjdk/samtools/filter/JavascriptSamRecordFilter.java
create mode 100644 src/java/htsjdk/samtools/util/ComparableTuple.java
copy src/java/htsjdk/samtools/util/{RuntimeEOFException.java => RuntimeScriptException.java} (73%)
create mode 100644 src/java/htsjdk/samtools/util/TrimmingUtil.java
create mode 100644 src/java/htsjdk/variant/variantcontext/filter/JavascriptVariantFilter.java
create mode 100644 src/tests/java/htsjdk/samtools/CRAMBAIIndexerTest.java
create mode 100644 src/tests/java/htsjdk/samtools/CRAMContainerStreamWriterTest.java
create mode 100644 src/tests/java/htsjdk/samtools/CRAMFileReaderTest.java
create mode 100644 src/tests/java/htsjdk/samtools/cram/LosslessRoundTripTest.java
create mode 100644 src/tests/java/htsjdk/samtools/cram/build/CompressionHeaderFactoryTest.java
create mode 100644 src/tests/java/htsjdk/samtools/cram/build/ContainerFactoryTest.java
create mode 100644 src/tests/java/htsjdk/samtools/cram/build/ContainerParserTest.java
create mode 100644 src/tests/java/htsjdk/samtools/cram/structure/SliceTests.java
create mode 100644 src/tests/java/htsjdk/samtools/fastq/FastqWriterTest.java
create mode 100644 src/tests/java/htsjdk/samtools/filter/JavascriptSamRecordFilterTest.java
create mode 100644 src/tests/java/htsjdk/samtools/sra/AbstractSRATest.java
create mode 100644 src/tests/java/htsjdk/samtools/sra/SRAAccessionTest.java
create mode 100644 src/tests/java/htsjdk/samtools/util/ComparableTupleTest.java
create mode 100644 src/tests/java/htsjdk/samtools/util/TrimmingUtilTest.java
create mode 100644 src/tests/java/htsjdk/samtools/util/TupleTest.java
create mode 100644 src/tests/java/htsjdk/variant/variantcontext/filter/JavascriptVariantFilterTest.java
create mode 100644 src/tests/java/htsjdk/variant/vcf/VCFHeaderLineUnitTest.java
create mode 120000 testdata/htsjdk/samtools/BAMFileIndexTest/symlink_with_index.bam
create mode 120000 testdata/htsjdk/samtools/BAMFileIndexTest/symlink_with_index.bam.bai
create mode 120000 testdata/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam
create mode 100644 testdata/htsjdk/samtools/ValidateSamFileTest/duplicated_reads.sam
create mode 100644 testdata/htsjdk/samtools/ValidateSamFileTest/duplicated_reads_out_of_order.sam
copy testdata/htsjdk/samtools/{cram/auxf#values.2.1.cram => cram_query_sorted.cram} (75%)
copy testdata/htsjdk/samtools/{cram_tlen.fasta => cram_query_sorted.fasta} (96%)
copy testdata/htsjdk/samtools/{cram_tlen.fasta.fai => cram_query_sorted.fasta.fai} (74%)
create mode 100644 testdata/htsjdk/samtools/samFilter01.js
create mode 100644 testdata/htsjdk/samtools/samFilter02.js
create mode 100644 testdata/htsjdk/variant/variantFilter01.js
create mode 100644 testdata/htsjdk/variant/variantFilter02.js
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