[med-svn] [picard-tools] branch upstream updated (711211f -> b8fee2b)
Charles Plessy
plessy at moszumanska.debian.org
Sat Mar 22 02:05:04 UTC 2014
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to branch upstream
in repository picard-tools.
from 711211f Imported Upstream version 1.105
new f1b1572 Imported Upstream version 1.106
new ec0f0f9 Imported Upstream version 1.107
new 5430f79 Imported Upstream version 1.108
new b8fee2b Imported Upstream version 1.109
The 4 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:
Picard-public.ipr | 2 +
build.xml | 15 +-
src/java/net/sf/picard/fastq/BasicFastqWriter.java | 4 +-
.../sf/picard/illumina/MarkIlluminaAdapters.java | 204 +++++-----
.../net/sf/picard/illumina/parser/BclParser.java | 16 +-
.../parser/ClusterIntensityFileReader.java | 2 +-
.../illumina/parser/CycleIlluminaFileMap.java | 59 ++-
.../parser/IlluminaDataProviderFactory.java | 69 ++--
.../picard/illumina/parser/IlluminaFileUtil.java | 212 ++++++++++-
.../illumina/parser/IlluminaIntensityParser.java | 2 +-
...on.java => MultiTileBclCycleFilesIterator.java} | 20 +-
.../picard/illumina/parser/MultiTileBclParser.java | 111 ++++++
...dDescriptor.java => MultiTileFilterParser.java} | 47 +--
.../illumina/parser/MultiTileLocsParser.java | 77 ++++
.../sf/picard/illumina/parser/MultiTileParser.java | 128 +++++++
.../sf/picard/illumina/parser/PerTileParser.java | 6 +-
.../illumina/parser/PerTilePerCycleParser.java | 5 +-
.../net/sf/picard/illumina/parser/TileIndex.java | 153 ++++++++
.../AbstractIlluminaPositionFileReader.java | 32 +-
.../illumina/parser/readers/BclIndexReader.java | 75 ++++
.../picard/illumina/parser/readers/BclReader.java | 31 +-
.../illumina/parser/readers/FilterFileReader.java | 4 +
.../illumina/parser/readers/LocsFileReader.java | 16 +-
.../parser/readers/MMapBackedIteratorFactory.java | 20 +
src/java/net/sf/picard/io/IoUtil.java | 23 +-
src/java/net/sf/picard/pedigree/PedFile.java | 76 +++-
src/java/net/sf/picard/pedigree/PedTrio.java | 45 ---
.../reference/ReferenceSequenceFileFactory.java | 2 +
.../net/sf/picard/sam/AbstractAlignmentMerger.java | 130 ++++---
src/java/net/sf/picard/sam/CleanSam.java | 19 +-
src/java/net/sf/picard/sam/HitsForInsert.java | 5 +
src/java/net/sf/picard/sam/MarkDuplicates.java | 4 +-
src/java/net/sf/picard/sam/MergeBamAlignment.java | 10 +-
.../sf/picard/sam/MultiHitAlignedReadIterator.java | 54 ++-
src/java/net/sf/picard/sam/ReorderSam.java | 9 +-
...RevertOriginalBaseQualitiesAndAddMateCigar.java | 234 ++++++++++++
src/java/net/sf/picard/sam/RevertSam.java | 232 +++++++++---
src/java/net/sf/picard/sam/SamAlignmentMerger.java | 55 ++-
src/java/net/sf/picard/sam/SamFileValidator.java | 43 ++-
src/java/net/sf/picard/sam/SamFormatConverter.java | 2 +-
src/java/net/sf/picard/sam/SamPairUtil.java | 98 +++--
src/java/net/sf/picard/sam/SamToFastq.java | 301 +++++++++------
src/java/net/sf/picard/sam/SortSam.java | 2 +
src/java/net/sf/picard/util/IntervalListTools.java | 2 +-
.../net/sf/picard/util/ListMap.java} | 40 +-
src/java/net/sf/picard/util/MathUtil.java | 16 +-
src/java/net/sf/picard/util/ProgressLogger.java | 27 +-
src/java/net/sf/picard/util/SamLocusIterator.java | 11 +-
.../sf/picard/util/SamRecordIntervalIterator.java | 188 ---------
.../util/SamRecordIntervalIteratorFactory.java | 13 +-
src/java/net/sf/picard/vcf/MakeSitesOnlyVcf.java | 28 +-
src/java/net/sf/picard/vcf/VcfFormatConverter.java | 8 +-
src/java/net/sf/samtools/AbstractBAMFileIndex.java | 114 +++---
src/java/net/sf/samtools/AsyncSAMFileWriter.java | 13 +-
src/java/net/sf/samtools/BAMFileReader.java | 419 ++++++++++++++-------
src/java/net/sf/samtools/CachingBAMFileIndex.java | 34 +-
src/java/net/sf/samtools/Chunk.java | 50 ++-
.../net/sf/samtools/DiskBasedBAMFileIndex.java | 14 +-
src/java/net/sf/samtools/SAMFileHeader.java | 5 +-
src/java/net/sf/samtools/SAMFileReader.java | 224 ++++++++++-
src/java/net/sf/samtools/SAMFileSpan.java | 48 +--
src/java/net/sf/samtools/SAMFileWriter.java | 11 +-
src/java/net/sf/samtools/SAMFileWriterFactory.java | 42 ++-
src/java/net/sf/samtools/SAMFileWriterImpl.java | 14 +-
.../net/sf/samtools/SAMHeaderRecordComparator.java | 66 ++++
src/java/net/sf/samtools/SAMRecord.java | 267 ++++++++++---
src/java/net/sf/samtools/SAMRecordSetBuilder.java | 14 +-
src/java/net/sf/samtools/SAMRecordUtil.java | 1 -
src/java/net/sf/samtools/SAMTag.java | 2 +-
src/java/net/sf/samtools/SAMTagUtil.java | 66 ++--
src/java/net/sf/samtools/SAMTextReader.java | 5 +
src/java/net/sf/samtools/SAMUtils.java | 65 ++++
src/java/net/sf/samtools/SAMValidationError.java | 42 ++-
.../net/sf/samtools/util/AbstractAsyncWriter.java | 3 +
.../samtools/util/BlockCompressedInputStream.java | 15 +-
src/java/net/sf/samtools/util/Lazy.java | 4 +
.../ProgressLoggerInterface.java} | 31 +-
src/java/net/sf/samtools/util/TestUtil.java | 19 +-
src/java/org/broad/tribble/util/TabixUtils.java | 50 +++
.../org/broadinstitute/variant/bcf2/BCF2Utils.java | 5 +
.../variant/variantcontext/Allele.java | 17 +-
.../variant/variantcontext/VariantContext.java | 55 ++-
.../variantcontext/VariantContextBuilder.java | 17 +-
.../writer/AsyncVariantContextWriter.java | 49 +++
.../variantcontext/writer/BCF2FieldEncoder.java | 16 +-
.../variant/variantcontext/writer/Options.java | 3 +-
.../writer/VariantContextWriterFactory.java | 177 +++++++--
.../variant/vcf/AbstractVCFCodec.java | 35 +-
.../org/broadinstitute/variant/vcf/VCFCodec.java | 4 +-
.../variant/vcf/VCFCompoundHeaderLine.java | 6 +-
.../broadinstitute/variant/vcf/VCFFileReader.java | 2 +-
.../variant/vcf/VCFHeaderLineTranslator.java | 1 +
.../variant/vcf/VCFHeaderVersion.java | 24 +-
.../illumina/parser/IlluminaFileUtilTest.java | 36 +-
.../illumina/parser/PerTilePerCycleParserTest.java | 2 +-
.../AbstractIlluminaPositionFileReaderTest.java | 4 +-
.../reference/ReferenceSequenceFileWalkerTest.java | 60 +++
src/tests/java/net/sf/picard/sam/CleanSamTest.java | 78 ++++
.../net/sf/picard/sam/MergeBamAlignmentTest.java | 23 +-
.../net/sf/picard/sam/ValidateSamFileTest.java | 68 ++--
.../java/net/sf/picard/vcf/MergeVcfsTest.java | 12 +-
.../net/sf/picard/vcf/VcfFormatConverterTest.java | 33 +-
.../java/net/sf/samtools/BAMFileIndexTest.java | 99 ++++-
.../sf/samtools/SamHeaderRecordComparatorTest.java | 72 ++++
.../variantcontext/VariantContextUnitTest.java | 41 +-
.../variantcontext/writer/VCFWriterUnitTest.java | 15 +-
.../intervallist/IntervalListFromVCFTest.vcf | 53 +++
.../IntervalListFromVCFTestComp.interval_list | 7 +
...ntervalListFromVCFTestCompInverse.interval_list | 10 +
...lListFromVCFTestCompInverseManual.interval_list | 10 +
.../intervallist/IntervalListFromVCFTestManual.vcf | 57 +++
...IntervalListFromVCFTestManualComp.interval_list | 12 +
.../sf/picard/sam/CleanSam/fits_with_deletion.sam | 3 +
.../sam/CleanSam/long_trailing_insertion.sam | 3 +
.../picard/sam/CleanSam/overhang_with_deletion.sam | 3 +
.../net/sf/picard/sam/CleanSam/simple_fits.sam | 3 +
.../net/sf/picard/sam/CleanSam/simple_overhang.sam | 3 +
.../sf/picard/sam/CleanSam/trailing_insertion.sam | 3 +
.../inappropriate_mate_cigar_string.sam} | 6 +-
.../invalid_mate_cigar_string.sam | 19 +
.../net/sf/picard/sam/mate_cigar_and_no_oqs.sam | 4 +
testdata/net/sf/picard/sam/mate_cigar_and_oqs.sam | 4 +
.../net/sf/picard/sam/no_mate_cigar_and_no_oqs.sam | 4 +
.../net/sf/picard/sam/no_mate_cigar_and_oqs.sam | 4 +
testdata/net/sf/picard/sam/no_mates_and_no_oqs.sam | 6 +
.../no_mates_and_no_oqs_in_first_four_records.sam | 7 +
testdata/net/sf/picard/sam/no_mates_and_oqs.sam | 6 +
127 files changed, 4370 insertions(+), 1436 deletions(-)
copy src/java/net/sf/picard/illumina/parser/{IlluminaFileNotFoundException.java => MultiTileBclCycleFilesIterator.java} (69%)
create mode 100644 src/java/net/sf/picard/illumina/parser/MultiTileBclParser.java
copy src/java/net/sf/picard/illumina/parser/{ReadDescriptor.java => MultiTileFilterParser.java} (53%)
create mode 100644 src/java/net/sf/picard/illumina/parser/MultiTileLocsParser.java
create mode 100644 src/java/net/sf/picard/illumina/parser/MultiTileParser.java
create mode 100644 src/java/net/sf/picard/illumina/parser/TileIndex.java
create mode 100644 src/java/net/sf/picard/illumina/parser/readers/BclIndexReader.java
delete mode 100644 src/java/net/sf/picard/pedigree/PedTrio.java
create mode 100644 src/java/net/sf/picard/sam/RevertOriginalBaseQualitiesAndAddMateCigar.java
copy src/{tests/java/net/sf/picard/util/RExecutorTest.java => java/net/sf/picard/util/ListMap.java} (66%)
delete mode 100644 src/java/net/sf/picard/util/SamRecordIntervalIterator.java
create mode 100644 src/java/net/sf/samtools/SAMHeaderRecordComparator.java
copy src/java/net/sf/samtools/{SAMFileWriter.java => util/ProgressLoggerInterface.java} (71%)
create mode 100644 src/java/org/broadinstitute/variant/variantcontext/writer/AsyncVariantContextWriter.java
create mode 100644 src/tests/java/net/sf/picard/reference/ReferenceSequenceFileWalkerTest.java
create mode 100644 src/tests/java/net/sf/picard/sam/CleanSamTest.java
create mode 100644 src/tests/java/net/sf/samtools/SamHeaderRecordComparatorTest.java
create mode 100644 testdata/net/sf/picard/intervallist/IntervalListFromVCFTest.vcf
create mode 100644 testdata/net/sf/picard/intervallist/IntervalListFromVCFTestComp.interval_list
create mode 100644 testdata/net/sf/picard/intervallist/IntervalListFromVCFTestCompInverse.interval_list
create mode 100644 testdata/net/sf/picard/intervallist/IntervalListFromVCFTestCompInverseManual.interval_list
create mode 100644 testdata/net/sf/picard/intervallist/IntervalListFromVCFTestManual.vcf
create mode 100644 testdata/net/sf/picard/intervallist/IntervalListFromVCFTestManualComp.interval_list
create mode 100644 testdata/net/sf/picard/sam/CleanSam/fits_with_deletion.sam
create mode 100644 testdata/net/sf/picard/sam/CleanSam/long_trailing_insertion.sam
create mode 100644 testdata/net/sf/picard/sam/CleanSam/overhang_with_deletion.sam
create mode 100644 testdata/net/sf/picard/sam/CleanSam/simple_fits.sam
create mode 100644 testdata/net/sf/picard/sam/CleanSam/simple_overhang.sam
create mode 100644 testdata/net/sf/picard/sam/CleanSam/trailing_insertion.sam
copy testdata/net/sf/picard/sam/{merger.dict => ValidateSamFileTest/inappropriate_mate_cigar_string.sam} (71%)
create mode 100644 testdata/net/sf/picard/sam/ValidateSamFileTest/invalid_mate_cigar_string.sam
create mode 100755 testdata/net/sf/picard/sam/mate_cigar_and_no_oqs.sam
create mode 100755 testdata/net/sf/picard/sam/mate_cigar_and_oqs.sam
create mode 100755 testdata/net/sf/picard/sam/no_mate_cigar_and_no_oqs.sam
create mode 100755 testdata/net/sf/picard/sam/no_mate_cigar_and_oqs.sam
create mode 100755 testdata/net/sf/picard/sam/no_mates_and_no_oqs.sam
create mode 100755 testdata/net/sf/picard/sam/no_mates_and_no_oqs_in_first_four_records.sam
create mode 100755 testdata/net/sf/picard/sam/no_mates_and_oqs.sam
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