[med-svn] [htsjdk] branch master updated (592b540 -> f53b9a9)
Vincent Danjean
vdanjean at debian.org
Mon Mar 14 20:11:31 UTC 2016
This is an automated email from the git hooks/post-receive script.
vdanjean pushed a change to branch master
in repository htsjdk.
from 592b540 Upload to unstable since build issues are solved
new a6a2d54 Imported Upstream version 2.1.1+dfsg.1
new a8546ae Merge tag 'upstream/2.1.1+dfsg.1' into sid
new 88069b2 New upstream version
new 684a7cb Update patches
new 5af3c7a Dump Standard-Version
new f53b9a9 Ready for upload
The 6 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 +-
debian/changelog | 6 +
debian/control | 2 +-
debian/patches/10-build.xml | 16 +-
debian/patches/13-skip_network_tests | 319 +++---
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 +
178 files changed, 6095 insertions(+), 2398 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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