[med-svn] [htsjdk] branch debian/jessie-backports updated (836c904 -> b768075)
Andreas Tille
tille at debian.org
Tue Apr 26 18:57:46 UTC 2016
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 836c904 Rebuild for jessie-backports.
adds 39fd256 rename (again) the source package
adds 800d414 Add get-orig-source target
adds ad6800c Imported Upstream version 2.0.1+dfsg.1
adds 19b7536 Merge tag 'upstream/2.0.1+dfsg.1'
adds ca64775 New upstream version
adds ecc9037 Adapt patches
adds cf96fea Seems htsjdk needs Open JDK 8 ... trying - but failed. :-(
adds eddb36c Merge remote-tracking branch 'origin/master' into sid
adds 57a90b3 add libngs-java dep
adds 6507102 set locale for tests
adds 3cd01be remove network tests to fix bug #808593
adds 7a326a8 skip more network tests
adds f4ad91d skip more network tests
adds bff963c skip more network tests
adds 3784ded skip more network tests
adds 92f3d46 remove network related tests
adds 62e447f debian/control: use https in Vcs-Git and Vcs-Browser
adds 592b540 Upload to unstable since build issues are solved
adds a6a2d54 Imported Upstream version 2.1.1+dfsg.1
adds a8546ae Merge tag 'upstream/2.1.1+dfsg.1' into sid
adds 88069b2 New upstream version
adds 684a7cb Update patches
adds 5af3c7a Dump Standard-Version
adds f53b9a9 Ready for upload
adds db7d8a5 Revert "Ready for upload"
adds 3237f28 Add a comment about the Debian specific revision
adds 1090487 Switch to default jdk now that it is >= 1.8
adds 4ab4b5c Make sure repackaged tarball is compressed with xz
adds 8f67825 Merge remote-tracking branch 'origin/master' into sid
adds 67511f6 default-jdk has an epoch for versionned dependency
adds a515a1f Upload to unstable
new 40634f7 Merge branch 'master' into debian/jessie-backports
new 3136fa0 Enforce openjdk 8
new b768075 Fix JAVA_HOME
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:
.github/ISSUE_TEMPLATE.md | 21 +
.github/PULL_REQUEST_TEMPLATE.md | 11 +
.idea/modules/htsjdk.iml | 3 +-
.travis.yml | 7 +-
README.md | 4 +
build.sbt | 8 +-
build.xml | 69 +-
debian/changelog | 31 +-
debian/control | 16 +-
.../01-for-upstream-fix-version-in-manifest | 16 -
debian/patches/10-build.xml | 28 +-
debian/patches/11-snappy-java-compatibility.patch | 2 +-
debian/patches/12-use_libjbzip2-java | 4 +-
debian/patches/13-skip_network_tests | 633 +++++++++++
debian/patches/series | 2 +-
debian/rules | 12 +-
debian/watch | 2 +-
htsjdk.iml | 9 +
src/java/htsjdk/samtools/AbstractBAMFileIndex.java | 27 +-
src/java/htsjdk/samtools/BAMFileReader.java | 2 +-
.../{SAMFileSpan.java => BAMFileSpan.java} | 59 +-
src/java/htsjdk/samtools/BAMFileWriter.java | 2 +-
src/java/htsjdk/samtools/BAMIndexMetaData.java | 4 +-
src/java/htsjdk/samtools/BAMRecord.java | 7 +-
src/java/htsjdk/samtools/BAMRecordCodec.java | 6 +-
src/java/htsjdk/samtools/BamIndexValidator.java | 88 +-
src/java/htsjdk/samtools/BinaryTagCodec.java | 11 +-
...eWriter.java => CRAMContainerStreamWriter.java} | 333 +++---
src/java/htsjdk/samtools/CRAMFileReader.java | 210 +++-
src/java/htsjdk/samtools/CRAMFileWriter.java | 412 ++------
src/java/htsjdk/samtools/CRAMIndexer.java | 166 ++-
src/java/htsjdk/samtools/CRAMIterator.java | 56 +-
.../samtools/ChainedDownsamplingIterator.java | 90 ++
src/java/htsjdk/samtools/Cigar.java | 85 +-
src/java/htsjdk/samtools/CigarElement.java | 5 +
src/java/htsjdk/samtools/CigarOperator.java | 25 +
.../ConstantMemoryDownsamplingIterator.java | 88 ++
.../htsjdk/samtools/DefaultSAMRecordFactory.java | 6 +-
src/java/htsjdk/samtools/Defaults.java | 4 +-
.../htsjdk/samtools/DiskBasedBAMFileIndex.java | 8 +-
src/java/htsjdk/samtools/DownsamplingIterator.java | 164 ++-
.../samtools/DownsamplingIteratorFactory.java | 118 +++
.../htsjdk/samtools/DuplicateScoringStrategy.java | 39 +-
src/java/htsjdk/samtools/DuplicateSet.java | 70 +-
src/java/htsjdk/samtools/DuplicateSetIterator.java | 16 +-
.../samtools/HighAccuracyDownsamplingIterator.java | 196 ++++
.../htsjdk/samtools/MergingSamRecordIterator.java | 16 +-
.../SAMBinaryTagAndUnsignedArrayValue.java | 14 +-
src/java/htsjdk/samtools/SAMBinaryTagAndValue.java | 43 +-
src/java/htsjdk/samtools/SAMFileSpan.java | 244 -----
src/java/htsjdk/samtools/SAMFileWriterFactory.java | 200 +++-
src/java/htsjdk/samtools/SAMFileWriterImpl.java | 20 +-
.../htsjdk/samtools/SAMHeaderRecordComparator.java | 4 +-
src/java/htsjdk/samtools/SAMLineParser.java | 4 +-
src/java/htsjdk/samtools/SAMRecord.java | 769 +++++++++++---
.../samtools/SAMRecordCoordinateComparator.java | 12 +-
.../samtools/SAMRecordDuplicateComparator.java | 51 +-
.../samtools/SAMRecordQueryHashComparator.java | 72 ++
.../samtools/SAMRecordQueryNameComparator.java | 5 +-
src/java/htsjdk/samtools/SAMTag.java | 3 +
src/java/htsjdk/samtools/SAMTextHeaderCodec.java | 2 +-
src/java/htsjdk/samtools/SAMUtils.java | 189 +++-
src/java/htsjdk/samtools/SAMValidationError.java | 3 +-
src/java/htsjdk/samtools/SRAFileReader.java | 306 ++++++
src/java/htsjdk/samtools/SRAIndex.java | 257 +++++
src/java/htsjdk/samtools/SRAIterator.java | 248 +++++
src/java/htsjdk/samtools/SamFileHeaderMerger.java | 2 +-
src/java/htsjdk/samtools/SamFileValidator.java | 45 +-
src/java/htsjdk/samtools/SamFiles.java | 55 +-
src/java/htsjdk/samtools/SamIndexes.java | 94 ++
src/java/htsjdk/samtools/SamInputResource.java | 68 +-
src/java/htsjdk/samtools/SamPairUtil.java | 55 +-
src/java/htsjdk/samtools/SamReader.java | 1 +
src/java/htsjdk/samtools/SamReaderFactory.java | 72 +-
src/java/htsjdk/samtools/SamStreams.java | 1 +
src/java/htsjdk/samtools/TextTagCodec.java | 31 +-
.../htsjdk/samtools/TextualBAMIndexWriter.java | 2 +-
src/java/htsjdk/samtools/cram/CRAIEntry.java | 148 +++
src/java/htsjdk/samtools/cram/CRAIIndex.java | 164 +++
src/java/htsjdk/samtools/cram/CRAMException.java | 22 +
.../cram/build/CompressionHeaderFactory.java | 1118 ++++++++------------
.../samtools/cram/build/ContainerFactory.java | 29 +-
.../samtools/cram/build/ContainerParser.java | 88 +-
src/java/htsjdk/samtools/cram/build/CramIO.java | 34 +-
.../htsjdk/samtools/cram/build/CramNormalizer.java | 3 +
.../samtools/cram/build/Sam2CramRecordFactory.java | 15 +-
.../htsjdk/samtools/cram/common/CramVersions.java | 6 +-
.../codec/CanonicalHuffmanIntegerCodec.java | 8 +-
.../huffman/codec/HuffmanParamsCalculator.java | 137 +++
.../cram/encoding/reader/CramRecordReader.java | 22 +-
.../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 | 46 +-
.../samtools/cram/structure/AlignmentSpan.java | 92 ++
.../htsjdk/samtools/cram/structure/Container.java | 12 +-
.../cram/structure/CramCompressionRecord.java | 16 +-
.../htsjdk/samtools/cram/structure/ReadTag.java | 30 +-
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 +++
.../htsjdk/samtools/filter/FilteringIterator.java | 2 +-
.../htsjdk/samtools/filter/IntervalFilter.java | 2 +-
.../samtools/filter/JavascriptSamRecordFilter.java | 101 ++
.../samtools/filter/OverclippedReadFilter.java | 76 ++
src/java/htsjdk/samtools/metrics/MetricBase.java | 4 +-
src/java/htsjdk/samtools/metrics/MetricsFile.java | 42 +-
.../reference/AbstractFastaSequenceFile.java | 76 +-
.../samtools/reference/FastaSequenceFile.java | 18 +-
.../samtools/reference/FastaSequenceIndex.java | 21 +-
.../reference/IndexedFastaSequenceFile.java | 98 +-
.../reference/ReferenceSequenceFileFactory.java | 45 +-
.../seekablestream/SeekableMemoryStream.java | 64 ++
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 +++
src/java/htsjdk/samtools/sra/SRALazyRecord.java | 1056 ++++++++++++++++++
.../samtools/sra/SRAUnalignmentIterator.java | 181 ++++
src/java/htsjdk/samtools/sra/SRAUtils.java | 83 ++
.../htsjdk/samtools/util/AbstractAsyncWriter.java | 2 +-
.../samtools/util/AbstractProgressLogger.java | 10 +-
src/java/htsjdk/samtools/util/BinaryCodec.java | 18 +-
.../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 | 14 +-
src/java/htsjdk/samtools/util/FormatUtil.java | 2 +-
src/java/htsjdk/samtools/util/Histogram.java | 20 +-
src/java/htsjdk/samtools/util/IOUtil.java | 66 +-
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 | 119 +++
src/java/htsjdk/samtools/util/ProcessExecutor.java | 2 +-
src/java/htsjdk/samtools/util/ProgressLogger.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 | 214 +++-
.../htsjdk/samtools/util/SortingCollection.java | 4 +-
.../samtools/util/SortingLongCollection.java | 4 +-
src/java/htsjdk/samtools/util/StringUtil.java | 16 +-
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 | 47 +-
.../variantcontext/VariantContextBuilder.java | 14 +-
.../variantcontext/VariantContextComparator.java | 8 +-
.../variantcontext/VariantContextUtils.java | 62 +-
.../variantcontext/filter/CompoundFilter.java | 74 ++
.../variantcontext/filter/FilteringIterator.java | 127 +++
.../filter/GenotypeQualityFilter.java | 79 ++
.../filter/HeterozygosityFilter.java | 84 ++
.../filter/JavascriptVariantFilter.java | 97 ++
.../filter/PassingVariantFilter.java} | 23 +-
.../variantcontext/filter/SnpFilter.java} | 27 +-
.../filter/VariantContextFilter.java} | 26 +-
.../variant/variantcontext/writer/BCF2Encoder.java | 2 +-
.../variantcontext/writer/BCF2FieldEncoder.java | 35 +-
.../writer/SortingVariantContextWriterBase.java | 5 +-
.../writer/VariantContextWriterBuilder.java | 25 +-
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/VCFRecordCodec.java | 18 +-
src/java/htsjdk/variant/vcf/VCFUtils.java | 2 +-
.../java/htsjdk/samtools/BAMFileWriterTest.java | 135 ++-
.../java/htsjdk/samtools/CRAMBAIIndexerTest.java | 87 ++
.../java/htsjdk/samtools/CRAMComplianceTest.java | 11 +-
.../samtools/CRAMContainerStreamWriterTest.java | 184 ++++
.../java/htsjdk/samtools/CRAMEdgeCasesTest.java | 33 +-
.../java/htsjdk/samtools/CRAMFileIndexTest.java | 104 +-
.../java/htsjdk/samtools/CRAMFileReaderTest.java | 163 +++
.../samtools/CRAMFileWriterWithIndexTest.java | 9 +-
src/tests/java/htsjdk/samtools/CigarTest.java | 105 +-
.../java/htsjdk/samtools/CramFileWriterTest.java | 170 ++-
.../htsjdk/samtools/DownsamplingIteratorTests.java | 82 ++
.../htsjdk/samtools/DuplicateSetIteratorTest.java | 5 +-
.../samtools/MergingSamRecordIteratorTest.java | 41 +
.../java/htsjdk/samtools/SAMFileReaderTest.java | 69 +-
.../htsjdk/samtools/SAMFileWriterFactoryTest.java | 159 ++-
.../java/htsjdk/samtools/SAMIntegerTagTest.java | 167 ++-
.../samtools/SAMRecordDuplicateComparatorTest.java | 15 +
.../java/htsjdk/samtools/SAMRecordUnitTest.java | 957 ++++++++++++++++-
.../java/htsjdk/samtools/SAMTextWriterTest.java | 12 +
src/tests/java/htsjdk/samtools/SAMUtilsTest.java | 131 +++
src/tests/java/htsjdk/samtools/SamFilesTest.java | 81 ++
src/tests/java/htsjdk/samtools/SamIndexesTest.java | 192 ++++
.../java/htsjdk/samtools/SamReaderFactoryTest.java | 25 +
src/tests/java/htsjdk/samtools/SamSpecIntTest.java | 4 +-
.../java/htsjdk/samtools/ValidateSamFileTest.java | 69 +-
.../java/htsjdk/samtools/cram/CRAIEntryTest.java | 145 +++
.../java/htsjdk/samtools/cram/CRAIIndexTest.java | 133 +++
.../samtools/cram/LosslessRoundTripTest.java | 68 ++
.../cram/build/CompressionHeaderFactoryTest.java | 208 ++++
.../samtools/cram/build/ContainerFactoryTest.java | 134 +++
.../samtools/cram/build/ContainerParserTest.java | 185 ++++
.../htsjdk/samtools/cram/build/CramIOTest.java | 82 ++
.../cram/encoding/huffman/codec/HuffmanTest.java | 18 +-
.../cram/structure/CramCompressionRecordTest.java | 68 ++
.../samtools/cram/structure/ReadTagTest.java | 21 +-
.../htsjdk/samtools/cram/structure/SliceTests.java | 36 +
.../htsjdk/samtools/fastq/FastqWriterTest.java | 73 ++
.../filter/JavascriptSamRecordFilterTest.java | 74 ++
.../samtools/filter/OverclippedReadFilterTest.java | 83 ++
.../htsjdk/samtools/metrics/MetricsFileTest.java | 21 +
.../samtools/reference/FastaSequenceIndexTest.java | 8 +-
.../reference/IndexedFastaSequenceFileTest.java | 10 +-
.../java/htsjdk/samtools/sra/AbstractSRATest.java | 57 +
.../java/htsjdk/samtools/sra/SRAAccessionTest.java | 29 +
.../java/htsjdk/samtools/sra/SRAIndexTest.java | 134 +++
.../htsjdk/samtools/sra/SRALazyRecordTest.java | 51 +
.../java/htsjdk/samtools/sra/SRAQueryTest.java | 73 ++
.../java/htsjdk/samtools/sra/SRAReferenceTest.java | 23 +
src/tests/java/htsjdk/samtools/sra/SRATest.java | 431 ++++++++
.../java/htsjdk/samtools/util/CodeUtilTest.java | 2 +-
.../htsjdk/samtools/util/ComparableTupleTest.java | 61 ++
.../htsjdk/samtools/util/DiskBackedQueueTest.java | 30 +-
src/tests/java/htsjdk/samtools/util/IupacTest.java | 2 +-
.../htsjdk/samtools/util/SequenceUtilTest.java | 256 ++++-
.../samtools/util/SortingCollectionTest.java | 39 +-
.../htsjdk/samtools/util/TrimmingUtilTest.java | 70 ++
src/tests/java/htsjdk/samtools/util/TupleTest.java | 62 ++
.../htsjdk/tribble/util/ftp/FTPClientTest.java | 77 +-
.../htsjdk/variant/bcf2/BCF2UtilsUnitTest.java | 25 +-
.../GenotypeLikelihoodsUnitTest.java | 161 ++-
.../variant/variantcontext/GenotypeUnitTest.java | 2 +
.../variantcontext/filter/AllFailFilter.java} | 27 +-
.../variantcontext/filter/AllPassFilter.java} | 20 +-
.../variantcontext/filter/CompoundFilterTest.java | 78 ++
.../filter/FilteringIteratorTest.java | 88 ++
.../filter/GenotypeQualityFilterTest.java | 105 ++
.../filter/HeterozygosityFilterTest.java | 128 +++
.../filter/JavascriptVariantFilterTest.java | 72 ++
.../filter/PassingVariantFilterTest.java | 46 +
.../variantcontext/filter/SnpFilterTest.java | 54 +
.../VariantContextWriterBuilderUnitTest.java | 10 +
.../htsjdk/variant/vcf/VCFHeaderLineUnitTest.java | 43 +
.../java/htsjdk/variant/vcf/VCFHeaderUnitTest.java | 135 ++-
.../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 +
.../testContigNotInRef.cram} | Bin
.../testContigNotInRef.cram.bai} | Bin
.../testContigNotInRef.dict} | 2 +-
.../testContigNotInRef.fa} | 2 +-
.../cram/CRAMException/testContigNotInRef.fa.fai | 1 +
.../testContigNotInRef.fasta} | 0
.../c1#bounds.2.1.cram => cram_query_sorted.cram} | Bin 10508 -> 13266 bytes
testdata/htsjdk/samtools/cram_query_sorted.fasta | 40 +
.../htsjdk/samtools/cram_query_sorted.fasta.fai | 8 +
testdata/htsjdk/samtools/cram_tlen.fasta | 41 +
testdata/htsjdk/samtools/cram_tlen.fasta.fai | 8 +
.../valid.sam => cram_tlen_reads.sorted.sam} | 26 +-
testdata/htsjdk/samtools/cram_with_bai_index.cram | Bin 0 -> 4213 bytes
.../htsjdk/samtools/cram_with_bai_index.cram.bai | Bin 0 -> 336 bytes
testdata/htsjdk/samtools/cram_with_crai_index.cram | Bin 0 -> 4213 bytes
.../htsjdk/samtools/cram_with_crai_index.cram.crai | Bin 0 -> 77 bytes
testdata/htsjdk/samtools/hg19mini.fasta | 804 ++++++++++++++
testdata/htsjdk/samtools/hg19mini.fasta.fai | 4 +
.../htsjdk/samtools/metrics/metricsOne.metrics | 13 +
.../htsjdk/samtools/metrics/metricsOneCopy.metrics | 13 +
.../metrics/metricsOneModifiedHistogram.metrics | 14 +
.../metrics/metricsOneModifiedMetrics.metrics | 13 +
testdata/htsjdk/samtools/samFilter01.js | 2 +
testdata/htsjdk/samtools/samFilter02.js | 9 +
testdata/htsjdk/samtools/sra/test_archive.sra | Bin 0 -> 1099831 bytes
testdata/htsjdk/variant/variantFilter01.js | 2 +
testdata/htsjdk/variant/variantFilter02.js | 20 +
293 files changed, 17588 insertions(+), 3031 deletions(-)
create mode 100644 .github/ISSUE_TEMPLATE.md
create mode 100644 .github/PULL_REQUEST_TEMPLATE.md
delete mode 100644 debian/patches/01-for-upstream-fix-version-in-manifest
create mode 100644 debian/patches/13-skip_network_tests
copy src/java/htsjdk/samtools/{SAMFileSpan.java => BAMFileSpan.java} (83%)
copy src/java/htsjdk/samtools/{CRAMFileWriter.java => CRAMContainerStreamWriter.java} (73%)
create mode 100644 src/java/htsjdk/samtools/ChainedDownsamplingIterator.java
create mode 100644 src/java/htsjdk/samtools/ConstantMemoryDownsamplingIterator.java
create mode 100644 src/java/htsjdk/samtools/DownsamplingIteratorFactory.java
create mode 100644 src/java/htsjdk/samtools/HighAccuracyDownsamplingIterator.java
create mode 100644 src/java/htsjdk/samtools/SAMRecordQueryHashComparator.java
create mode 100644 src/java/htsjdk/samtools/SRAFileReader.java
create mode 100644 src/java/htsjdk/samtools/SRAIndex.java
create mode 100644 src/java/htsjdk/samtools/SRAIterator.java
create mode 100644 src/java/htsjdk/samtools/SamIndexes.java
create mode 100644 src/java/htsjdk/samtools/cram/CRAIEntry.java
create mode 100644 src/java/htsjdk/samtools/cram/CRAIIndex.java
create mode 100644 src/java/htsjdk/samtools/cram/CRAMException.java
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/filter/OverclippedReadFilter.java
create mode 100644 src/java/htsjdk/samtools/seekablestream/SeekableMemoryStream.java
create mode 100644 src/java/htsjdk/samtools/sra/ReferenceCache.java
create mode 100644 src/java/htsjdk/samtools/sra/SRAAccession.java
create mode 100644 src/java/htsjdk/samtools/sra/SRAAlignmentIterator.java
create mode 100644 src/java/htsjdk/samtools/sra/SRAIndexedSequenceFile.java
create mode 100644 src/java/htsjdk/samtools/sra/SRALazyRecord.java
create mode 100644 src/java/htsjdk/samtools/sra/SRAUnalignmentIterator.java
create mode 100644 src/java/htsjdk/samtools/sra/SRAUtils.java
create mode 100644 src/java/htsjdk/samtools/util/ComparableTuple.java
create mode 100644 src/java/htsjdk/samtools/util/Murmur3.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/CompoundFilter.java
create mode 100644 src/java/htsjdk/variant/variantcontext/filter/FilteringIterator.java
create mode 100644 src/java/htsjdk/variant/variantcontext/filter/GenotypeQualityFilter.java
create mode 100644 src/java/htsjdk/variant/variantcontext/filter/HeterozygosityFilter.java
create mode 100644 src/java/htsjdk/variant/variantcontext/filter/JavascriptVariantFilter.java
copy src/java/htsjdk/{tribble/Feature.java => variant/variantcontext/filter/PassingVariantFilter.java} (65%)
copy src/java/htsjdk/{tribble/readers/LineReader.java => variant/variantcontext/filter/SnpFilter.java} (67%)
copy src/java/htsjdk/{tribble/Feature.java => variant/variantcontext/filter/VariantContextFilter.java} (69%)
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/DownsamplingIteratorTests.java
create mode 100644 src/tests/java/htsjdk/samtools/SamFilesTest.java
create mode 100644 src/tests/java/htsjdk/samtools/SamIndexesTest.java
create mode 100644 src/tests/java/htsjdk/samtools/cram/CRAIEntryTest.java
create mode 100644 src/tests/java/htsjdk/samtools/cram/CRAIIndexTest.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/build/CramIOTest.java
create mode 100644 src/tests/java/htsjdk/samtools/cram/structure/CramCompressionRecordTest.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/filter/OverclippedReadFilterTest.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/sra/SRAIndexTest.java
create mode 100644 src/tests/java/htsjdk/samtools/sra/SRALazyRecordTest.java
create mode 100644 src/tests/java/htsjdk/samtools/sra/SRAQueryTest.java
create mode 100644 src/tests/java/htsjdk/samtools/sra/SRAReferenceTest.java
create mode 100644 src/tests/java/htsjdk/samtools/sra/SRATest.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
copy src/{java/htsjdk/samtools/SAMException.java => tests/java/htsjdk/variant/variantcontext/filter/AllFailFilter.java} (71%)
copy src/{java/htsjdk/tribble/index/TribbleIndexCreator.java => tests/java/htsjdk/variant/variantcontext/filter/AllPassFilter.java} (72%)
create mode 100644 src/tests/java/htsjdk/variant/variantcontext/filter/CompoundFilterTest.java
create mode 100644 src/tests/java/htsjdk/variant/variantcontext/filter/FilteringIteratorTest.java
create mode 100644 src/tests/java/htsjdk/variant/variantcontext/filter/GenotypeQualityFilterTest.java
create mode 100644 src/tests/java/htsjdk/variant/variantcontext/filter/HeterozygosityFilterTest.java
create mode 100644 src/tests/java/htsjdk/variant/variantcontext/filter/JavascriptVariantFilterTest.java
create mode 100644 src/tests/java/htsjdk/variant/variantcontext/filter/PassingVariantFilterTest.java
create mode 100644 src/tests/java/htsjdk/variant/variantcontext/filter/SnpFilterTest.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/{test.cram => CRAMException/testContigNotInRef.cram} (100%)
copy testdata/htsjdk/samtools/cram/{test.cram.bai => CRAMException/testContigNotInRef.cram.bai} (100%)
copy testdata/htsjdk/samtools/cram/{test.dict => CRAMException/testContigNotInRef.dict} (59%)
copy testdata/htsjdk/samtools/cram/{auxf.fa => CRAMException/testContigNotInRef.fa} (72%)
create mode 100644 testdata/htsjdk/samtools/cram/CRAMException/testContigNotInRef.fa.fai
copy testdata/htsjdk/samtools/cram/{auxf.fa => CRAMException/testContigNotInRef.fasta} (100%)
copy testdata/htsjdk/samtools/{cram/c1#bounds.2.1.cram => cram_query_sorted.cram} (75%)
create mode 100644 testdata/htsjdk/samtools/cram_query_sorted.fasta
create mode 100644 testdata/htsjdk/samtools/cram_query_sorted.fasta.fai
create mode 100644 testdata/htsjdk/samtools/cram_tlen.fasta
create mode 100644 testdata/htsjdk/samtools/cram_tlen.fasta.fai
copy testdata/htsjdk/samtools/{ValidateSamFileTest/valid.sam => cram_tlen_reads.sorted.sam} (55%)
create mode 100644 testdata/htsjdk/samtools/cram_with_bai_index.cram
create mode 100644 testdata/htsjdk/samtools/cram_with_bai_index.cram.bai
create mode 100644 testdata/htsjdk/samtools/cram_with_crai_index.cram
create mode 100644 testdata/htsjdk/samtools/cram_with_crai_index.cram.crai
create mode 100644 testdata/htsjdk/samtools/hg19mini.fasta
create mode 100644 testdata/htsjdk/samtools/hg19mini.fasta.fai
create mode 100644 testdata/htsjdk/samtools/metrics/metricsOne.metrics
create mode 100644 testdata/htsjdk/samtools/metrics/metricsOneCopy.metrics
create mode 100644 testdata/htsjdk/samtools/metrics/metricsOneModifiedHistogram.metrics
create mode 100644 testdata/htsjdk/samtools/metrics/metricsOneModifiedMetrics.metrics
create mode 100644 testdata/htsjdk/samtools/samFilter01.js
create mode 100644 testdata/htsjdk/samtools/samFilter02.js
create mode 100644 testdata/htsjdk/samtools/sra/test_archive.sra
create mode 100644 testdata/htsjdk/variant/variantFilter01.js
create mode 100644 testdata/htsjdk/variant/variantFilter02.js
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