[med-svn] [htsjdk] branch upstream updated (caea0dc -> ad6800c)
Andreas Tille
tille at debian.org
Sat Dec 19 21:26:58 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository htsjdk.
from caea0dc Imported Upstream version 1.138+dfsg.1
new ad6800c Imported Upstream version 2.0.1+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:
.idea/modules/htsjdk.iml | 3 +-
.travis.yml | 5 +-
README.md | 2 +
build.sbt | 8 +-
build.xml | 9 +-
htsjdk.iml | 9 +
src/java/htsjdk/samtools/AbstractBAMFileIndex.java | 27 +-
.../{SAMFileSpan.java => BAMFileSpan.java} | 59 +-
src/java/htsjdk/samtools/BAMRecord.java | 7 +-
src/java/htsjdk/samtools/BAMRecordCodec.java | 6 +-
src/java/htsjdk/samtools/BinaryTagCodec.java | 11 +-
src/java/htsjdk/samtools/CRAMFileReader.java | 64 +-
src/java/htsjdk/samtools/CRAMFileWriter.java | 99 +-
src/java/htsjdk/samtools/CRAMIndexer.java | 36 +-
src/java/htsjdk/samtools/CRAMIterator.java | 34 +-
.../samtools/ChainedDownsamplingIterator.java | 90 ++
.../ConstantMemoryDownsamplingIterator.java | 88 ++
.../htsjdk/samtools/DefaultSAMRecordFactory.java | 6 +-
src/java/htsjdk/samtools/DownsamplingIterator.java | 164 ++-
.../samtools/DownsamplingIteratorFactory.java | 118 +++
.../htsjdk/samtools/DuplicateScoringStrategy.java | 39 +-
src/java/htsjdk/samtools/DuplicateSet.java | 70 +-
.../samtools/HighAccuracyDownsamplingIterator.java | 196 ++++
.../htsjdk/samtools/MergingSamRecordIterator.java | 12 +-
.../SAMBinaryTagAndUnsignedArrayValue.java | 14 +-
src/java/htsjdk/samtools/SAMBinaryTagAndValue.java | 43 +-
src/java/htsjdk/samtools/SAMFileSpan.java | 244 -----
src/java/htsjdk/samtools/SAMFileWriterFactory.java | 149 ++-
src/java/htsjdk/samtools/SAMFileWriterImpl.java | 20 +-
src/java/htsjdk/samtools/SAMRecord.java | 680 ++++++++++---
.../samtools/SAMRecordCoordinateComparator.java | 6 +
.../samtools/SAMRecordDuplicateComparator.java | 46 +-
.../samtools/SAMRecordQueryHashComparator.java | 68 ++
src/java/htsjdk/samtools/SAMTag.java | 3 +
src/java/htsjdk/samtools/SAMUtils.java | 174 +++-
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/SamFileValidator.java | 21 +-
src/java/htsjdk/samtools/SamFiles.java | 23 +-
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 | 47 +-
src/java/htsjdk/samtools/SamStreams.java | 1 +
src/java/htsjdk/samtools/TextTagCodec.java | 19 +-
src/java/htsjdk/samtools/cram/CRAIEntry.java | 148 +++
src/java/htsjdk/samtools/cram/CRAIIndex.java | 164 +++
src/java/htsjdk/samtools/cram/CRAMException.java | 22 +
.../samtools/cram/build/ContainerParser.java | 13 +-
src/java/htsjdk/samtools/cram/build/CramIO.java | 10 +-
.../samtools/cram/build/Sam2CramRecordFactory.java | 13 +
.../cram/encoding/reader/CramRecordReader.java | 22 +-
.../htsjdk/samtools/cram/ref/ReferenceSource.java | 9 +-
.../cram/structure/CramCompressionRecord.java | 6 +-
.../htsjdk/samtools/cram/structure/ReadTag.java | 30 +-
.../htsjdk/samtools/filter/FilteringIterator.java | 2 +-
.../htsjdk/samtools/filter/IntervalFilter.java | 2 +-
.../samtools/filter/OverclippedReadFilter.java | 76 ++
src/java/htsjdk/samtools/metrics/MetricsFile.java | 32 +-
.../reference/AbstractFastaSequenceFile.java | 74 +-
.../samtools/reference/FastaSequenceFile.java | 18 +-
.../samtools/reference/FastaSequenceIndex.java | 21 +-
.../reference/IndexedFastaSequenceFile.java | 96 +-
.../reference/ReferenceSequenceFileFactory.java | 45 +-
.../seekablestream/SeekableMemoryStream.java | 64 ++
src/java/htsjdk/samtools/sra/ReferenceCache.java | 79 ++
src/java/htsjdk/samtools/sra/SRAAccession.java | 108 ++
.../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 | 2 +-
src/java/htsjdk/samtools/util/BinaryCodec.java | 10 +-
src/java/htsjdk/samtools/util/DiskBackedQueue.java | 12 +-
src/java/htsjdk/samtools/util/Histogram.java | 20 +-
src/java/htsjdk/samtools/util/IOUtil.java | 62 +-
src/java/htsjdk/samtools/util/Murmur3.java | 115 +++
src/java/htsjdk/samtools/util/ProgressLogger.java | 2 +-
src/java/htsjdk/samtools/util/SequenceUtil.java | 57 +-
src/java/htsjdk/samtools/util/StringUtil.java | 4 +-
.../variant/variantcontext/VariantContext.java | 8 +-
.../variantcontext/filter/CompoundFilter.java | 74 ++
.../variantcontext/filter/FilteringIterator.java | 127 +++
.../filter/GenotypeQualityFilter.java | 79 ++
.../filter/HeterozygosityFilter.java | 84 ++
.../filter/PassingVariantFilter.java} | 23 +-
.../variantcontext/filter/SnpFilter.java} | 23 +-
.../filter/VariantContextFilter.java} | 26 +-
.../variantcontext/writer/BCF2FieldEncoder.java | 35 +-
.../writer/VariantContextWriterBuilder.java | 25 +-
src/java/htsjdk/variant/vcf/VCFRecordCodec.java | 18 +-
.../java/htsjdk/samtools/BAMFileWriterTest.java | 133 ++-
.../java/htsjdk/samtools/CRAMComplianceTest.java | 7 +-
.../java/htsjdk/samtools/CRAMEdgeCasesTest.java | 33 +-
.../java/htsjdk/samtools/CRAMFileIndexTest.java | 66 ++
.../samtools/CRAMFileWriterWithIndexTest.java | 3 +-
src/tests/java/htsjdk/samtools/CigarTest.java | 81 +-
.../java/htsjdk/samtools/CramFileWriterTest.java | 122 ++-
.../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 | 797 ++++++++++++++-
.../java/htsjdk/samtools/SAMTextWriterTest.java | 12 +
src/tests/java/htsjdk/samtools/SAMUtilsTest.java | 106 ++
src/tests/java/htsjdk/samtools/SamFilesTest.java | 60 ++
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/cram/CRAIEntryTest.java | 145 +++
.../java/htsjdk/samtools/cram/CRAIIndexTest.java | 133 +++
.../htsjdk/samtools/cram/build/CramIOTest.java | 82 ++
.../cram/structure/CramCompressionRecordTest.java | 68 ++
.../samtools/cram/structure/ReadTagTest.java | 21 +-
.../samtools/filter/OverclippedReadFilterTest.java | 83 ++
.../htsjdk/samtools/metrics/MetricsFileTest.java | 21 +
.../samtools/reference/FastaSequenceIndexTest.java | 8 +-
.../reference/IndexedFastaSequenceFileTest.java | 10 +-
.../java/htsjdk/samtools/sra/SRAIndexTest.java | 150 +++
.../htsjdk/samtools/sra/SRALazyRecordTest.java | 51 +
.../java/htsjdk/samtools/sra/SRAQueryTest.java | 116 +++
.../java/htsjdk/samtools/sra/SRAReferenceTest.java | 25 +
src/tests/java/htsjdk/samtools/sra/SRATest.java | 464 +++++++++
.../java/htsjdk/samtools/util/CodeUtilTest.java | 2 +-
.../htsjdk/samtools/util/DiskBackedQueueTest.java | 30 +-
.../htsjdk/samtools/util/SequenceUtilTest.java | 22 +
.../samtools/util/SortingCollectionTest.java | 39 +-
.../htsjdk/variant/bcf2/BCF2UtilsUnitTest.java | 25 +-
.../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/PassingVariantFilterTest.java | 46 +
.../variantcontext/filter/SnpFilterTest.java | 54 +
.../VariantContextWriterBuilderUnitTest.java | 10 +
.../java/htsjdk/variant/vcf/VCFHeaderUnitTest.java | 34 +-
.../testContigNotInRef.cram} | Bin
.../testContigNotInRef.cram.bai} | Bin
.../testContigNotInRef.dict} | 2 +-
.../testContigNotInRef.fa} | 2 +-
.../cram/CRAMException/testContigNotInRef.fa.fai | 1 +
.../testContigNotInRef.fasta} | 0
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/sra/test_archive.sra | Bin 0 -> 1099831 bytes
165 files changed, 11244 insertions(+), 1207 deletions(-)
copy src/java/htsjdk/samtools/{SAMFileSpan.java => BAMFileSpan.java} (83%)
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/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/Murmur3.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
copy src/java/htsjdk/{tribble/Feature.java => variant/variantcontext/filter/PassingVariantFilter.java} (65%)
copy src/java/htsjdk/{tribble/Feature.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/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/build/CramIOTest.java
create mode 100644 src/tests/java/htsjdk/samtools/cram/structure/CramCompressionRecordTest.java
create mode 100644 src/tests/java/htsjdk/samtools/filter/OverclippedReadFilterTest.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
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/PassingVariantFilterTest.java
create mode 100644 src/tests/java/htsjdk/variant/variantcontext/filter/SnpFilterTest.java
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%)
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/sra/test_archive.sra
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