[med-svn] [picard-tools] branch master updated (f458746 -> 544f221)
Charles Plessy
plessy at moszumanska.debian.org
Sat Mar 22 01:56:47 UTC 2014
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to branch master
in repository picard-tools.
from f458746 fix merge with Charles inputs
new efaffda Imported Upstream version 1.106
new e3eeb80 Merge tag 'upstream/1.106'
new 514b7eb Imported Upstream version 1.107
new 9cfa9d8 Merge tag 'upstream/1.107'
new 6ac75e2 Imported Upstream version 1.108
new 7abc4ce Merge tag 'upstream/1.108'
new a6e579a Imported Upstream version 1.109
new 89db57e Merge tag 'upstream/1.109'
new 544f221 New upstream releases; no new license nor copyright statement.
The 9 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 +-
debian/changelog | 6 +
debian/copyright | 4 +-
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 +-
.../{metrics/Header.java => util/ListMap.java} | 27 +-
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 +
129 files changed, 4376 insertions(+), 1427 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/java/net/sf/picard/{metrics/Header.java => util/ListMap.java} (66%)
mode change 100644 => 100755
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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