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Viewing all changes in revision 4.

Committer: Bazaar Package Importer
Author(s): Shaun Jackman
Date: 2011-03-22 10:52:23 UTC
mfrom: (1.1.2 upstream)
Revision ID: james.westby@ubuntu.com-20110322105223-hmtmspfl16s0ubwv

Tags: 1.41-1

http://bugs.debian.org/619201

* New upstream release. Closes: #619201.
* Add five commands to bin/picard-tools and picard-tools.1.

files added:
src/java/net/sf/picard/analysis/CollectMultipleMetrics.java

src/java/net/sf/picard/analysis/SinglePassSamProgram.java

src/java/net/sf/picard/cmdline/CreateHtmlDocForStandardOptions.java

src/java/net/sf/picard/reference/ExtractSequences.java

src/java/net/sf/picard/sam/AddOrReplaceReadGroups.java

src/java/net/sf/picard/sam/BamIndexStats.java

src/java/net/sf/picard/sam/BuildBamIndex.java

src/java/net/sf/picard/sam/CoordinateSortedPairInfoMap.java

src/java/net/sf/picard/sam/ReorderSam.java

src/java/net/sf/picard/util/CollectionUtil.java

src/java/net/sf/picard/util/IntervalTreeMap.java

src/java/net/sf/samtools/BAMIndexMetaData.java

src/java/net/sf/samtools/BamIndexValidator.java

src/java/net/sf/samtools/util/BlockCompressedFilePointerUtil.java

src/java/net/sf/samtools/util/Md5CalculatingInputStream.java

src/java/net/sf/samtools/util/Md5CalculatingOutputStream.java

src/tests/java/net/sf/picard/util/HistogramTest.java

src/tests/java/net/sf/picard/util/IOUtilTest.java

src/tests/java/net/sf/samtools/BinTest.java

src/tests/java/net/sf/samtools/ChunkTest.java

src/tests/java/net/sf/samtools/SAMFileReaderTest.java

src/tests/java/net/sf/samtools/SAMFileWriterFactoryTest.java

src/tests/java/net/sf/samtools/util/BlockCompressedFilePointerUtilTest.java

testdata/net/sf/picard/sam/MergeBamAlignment

testdata/net/sf/picard/sam/MergeBamAlignment/aligned.badorder.sam

testdata/net/sf/picard/sam/MergeBamAlignment/allread1.trimmed.aligned.sam

testdata/net/sf/picard/sam/MergeBamAlignment/allread2.trimmed.aligned.sam

testdata/net/sf/picard/sam/MergeBamAlignment/firsthalf.read1.trimmed.aligned.sam

testdata/net/sf/picard/sam/MergeBamAlignment/firsthalf.read2.trimmed.aligned.sam

testdata/net/sf/picard/sam/MergeBamAlignment/multihit.aligned.sam

testdata/net/sf/picard/sam/MergeBamAlignment/multihit.unmapped.sam

testdata/net/sf/picard/sam/MergeBamAlignment/secondhalf.read1.trimmed.aligned.sam

testdata/net/sf/picard/sam/MergeBamAlignment/secondhalf.read2.trimmed.aligned.sam

testdata/net/sf/picard/sam/MergeBamAlignment/unmapped.badorder.sam

testdata/net/sf/picard/sam/MergeBamAlignment/unmapped.sam

testdata/net/sf/picard/sam/ValidateSamFileTest/bad_index.bai

testdata/net/sf/picard/sam/ValidateSamFileTest/bad_index.bam

testdata/net/sf/picard/sam/bam2fastq/paired/bad/grouped-unpaired-mate.sam

testdata/net/sf/picard/sam/bam2fastq/paired/ok/grouped-last-pair-mates-flipped.sam

testdata/net/sf/picard/sam/onehalfaligned.sam

testdata/net/sf/picard/sam/otherhalfaligned.sam

testdata/net/sf/picard/sam/summary_alignment_stats_test2.sam

testdata/net/sf/samtools/block_compressed.sam.gz

testdata/net/sf/samtools/compressed.bam

testdata/net/sf/samtools/compressed.sam.gz

testdata/net/sf/samtools/uncompressed.sam

files removed:
src/java/net/sf/picard/metrics/AggregateMetricCollector.java

src/java/net/sf/picard/metrics/MetricCollector.java

src/java/net/sf/picard/sam/CigarClippingIterator.java

src/java/net/sf/picard/util/BaiToText.java

src/java/net/sf/picard/util/BamIndexStats.java

src/java/net/sf/picard/util/BuildBamIndex.java

src/java/net/sf/samtools/AbstractBAMIndexWriter.java

src/java/net/sf/samtools/BAMIndexBuilder.java

src/java/net/sf/samtools/BamIndexerForExistingBai.java

testdata/net/sf/samtools/BAMFileIndexTest/test_human.bai

files modified:
.pc/01-build.xml/build.xml

Picard-public.ipr

build.xml

debian/bin/picard-tools

debian/changelog

debian/picard-tools.1

src/java/net/sf/picard/analysis/CollectAlignmentSummaryMetrics.java

src/java/net/sf/picard/analysis/CollectGcBiasMetrics.java

src/java/net/sf/picard/analysis/CollectInsertSizeMetrics.java

src/java/net/sf/picard/analysis/MeanQualityByCycle.java

src/java/net/sf/picard/analysis/QualityScoreDistribution.java

src/java/net/sf/picard/analysis/directed/CalculateHsMetrics.java

src/java/net/sf/picard/analysis/directed/HsMetricsCalculator.java

src/java/net/sf/picard/cmdline/CommandLineParser.java

src/java/net/sf/picard/cmdline/CommandLineProgram.java

src/java/net/sf/picard/cmdline/CreateHtmlDocForProgram.java

src/java/net/sf/picard/cmdline/Option.java

src/java/net/sf/picard/fastq/BamToBfq.java

src/java/net/sf/picard/fastq/BamToBfqWriter.java

src/java/net/sf/picard/io/IoUtil.java

src/java/net/sf/picard/metrics/MetricBase.java

src/java/net/sf/picard/metrics/MetricsFile.java

src/java/net/sf/picard/reference/AbstractFastaSequenceFile.java

src/java/net/sf/picard/reference/IndexedFastaSequenceFile.java

src/java/net/sf/picard/reference/NormalizeFasta.java

src/java/net/sf/picard/reference/ReferenceSequenceFileFactory.java

src/java/net/sf/picard/sam/AbstractAlignmentMerger.java

src/java/net/sf/picard/sam/CleanSam.java

src/java/net/sf/picard/sam/DiskReadEndsMap.java

src/java/net/sf/picard/sam/DuplicationMetrics.java

src/java/net/sf/picard/sam/FastqToSam.java

src/java/net/sf/picard/sam/FixMateInformation.java

src/java/net/sf/picard/sam/MarkDuplicates.java

src/java/net/sf/picard/sam/MergeBamAlignment.java

src/java/net/sf/picard/sam/MergeSamFiles.java

src/java/net/sf/picard/sam/MergingSamRecordIterator.java

src/java/net/sf/picard/sam/ReservedTagConstants.java

src/java/net/sf/picard/sam/RevertSam.java

src/java/net/sf/picard/sam/SamAlignmentMerger.java

src/java/net/sf/picard/sam/SamFileValidator.java

src/java/net/sf/picard/sam/SamFormatConverter.java

src/java/net/sf/picard/sam/SamPairUtil.java

src/java/net/sf/picard/sam/SamToFastq.java

src/java/net/sf/picard/sam/ValidateSamFile.java

src/java/net/sf/picard/util/CigarUtil.java

src/java/net/sf/picard/util/FileAppendStreamLRUCache.java

src/java/net/sf/picard/util/FormatUtil.java

src/java/net/sf/picard/util/Histogram.java

src/java/net/sf/picard/util/Interval.java

src/java/net/sf/picard/util/IntervalList.java

src/java/net/sf/picard/util/Log.java

src/java/net/sf/picard/util/ResourceLimitedMapFunctor.java

src/java/net/sf/picard/util/SamRecordIntervalIteratorFactory.java

src/java/net/sf/samtools/AbstractBAMFileIndex.java

src/java/net/sf/samtools/AbstractSAMHeaderRecord.java

src/java/net/sf/samtools/BAMFileReader.java

src/java/net/sf/samtools/BAMFileWriter.java

src/java/net/sf/samtools/BAMIndex.java

src/java/net/sf/samtools/BAMIndexContent.java

src/java/net/sf/samtools/BAMIndexWriter.java

src/java/net/sf/samtools/BAMIndexer.java

src/java/net/sf/samtools/BAMRecord.java

src/java/net/sf/samtools/BAMRecordCodec.java

src/java/net/sf/samtools/Bin.java

src/java/net/sf/samtools/BinaryBAMIndexWriter.java

src/java/net/sf/samtools/BinaryTagCodec.java

src/java/net/sf/samtools/BrowseableBAMIndex.java

src/java/net/sf/samtools/CachingBAMFileIndex.java

src/java/net/sf/samtools/Chunk.java

src/java/net/sf/samtools/Cigar.java

src/java/net/sf/samtools/DiskBasedBAMFileIndex.java

src/java/net/sf/samtools/LinearIndex.java

src/java/net/sf/samtools/SAMBinaryTagAndValue.java

src/java/net/sf/samtools/SAMFileHeader.java

src/java/net/sf/samtools/SAMFileReader.java

src/java/net/sf/samtools/SAMFileSpan.java

src/java/net/sf/samtools/SAMFileWriterFactory.java

src/java/net/sf/samtools/SAMProgramRecord.java

src/java/net/sf/samtools/SAMReadGroupRecord.java

src/java/net/sf/samtools/SAMRecord.java

src/java/net/sf/samtools/SAMRecordCoordinateComparator.java

src/java/net/sf/samtools/SAMRecordQueryNameComparator.java

src/java/net/sf/samtools/SAMSequenceRecord.java

src/java/net/sf/samtools/SAMTextHeaderCodec.java

src/java/net/sf/samtools/SAMTextWriter.java

src/java/net/sf/samtools/SAMValidationError.java

src/java/net/sf/samtools/TextualBAMIndexWriter.java

src/java/net/sf/samtools/util/BlockCompressedInputStream.java

src/java/net/sf/samtools/util/BlockCompressedOutputStream.java

src/java/net/sf/samtools/util/IOUtil.java

src/java/net/sf/samtools/util/SeekableBufferedStream.java

src/java/net/sf/samtools/util/SeekableHTTPStream.java

src/java/net/sf/samtools/util/SequenceUtil.java

src/java/net/sf/samtools/util/StringUtil.java

src/scripts/release_picard.sh

src/tests/java/net/sf/picard/analysis/CollectAlignmentSummaryMetricsTest.java

src/tests/java/net/sf/picard/cmdline/CommandLineParserTest.java

src/tests/java/net/sf/picard/reference/IndexedFastaSequenceFileTest.java

src/tests/java/net/sf/picard/sam/FastqToSamTest.java

src/tests/java/net/sf/picard/sam/MergeBamAlignmentTest.java

src/tests/java/net/sf/picard/sam/SamFileHeaderMergerTest.java

src/tests/java/net/sf/picard/sam/SamToFastqTest.java

src/tests/java/net/sf/picard/sam/ValidateSamFileTest.java

src/tests/java/net/sf/picard/util/CigarUtilTest.java

src/tests/java/net/sf/samtools/BAMFileIndexTest.java

src/tests/java/net/sf/samtools/BAMIndexWriterTest.java

src/tests/java/net/sf/samtools/CigarTest.java

src/tests/java/net/sf/samtools/SAMTextReaderTest.java

src/tests/java/net/sf/samtools/SAMTextWriterTest.java

src/tests/java/net/sf/samtools/util/SequenceUtilTest.java

src/tests/java/net/sf/samtools/util/SortingCollectionTest.java

src/tests/java/net/sf/samtools/util/SortingLongCollectionTest.java

Show diffs side-by-side

added added

removed removed

.pc/01-build.xml/build.xml

Picard-public.ipr

debian/bin/picard-tools

debian/changelog

debian/picard-tools.1

src/java/net/sf/picard/analysis/CollectAlignmentSummaryMetrics.java

src/java/net/sf/picard/analysis/CollectGcBiasMetrics.java

src/java/net/sf/picard/analysis/CollectInsertSizeMetrics.java

src/java/net/sf/picard/analysis/CollectMultipleMetrics.java

src/java/net/sf/picard/analysis/MeanQualityByCycle.java

src/java/net/sf/picard/analysis/QualityScoreDistribution.java

src/java/net/sf/picard/analysis/SinglePassSamProgram.java

src/java/net/sf/picard/analysis/directed/CalculateHsMetrics.java

src/java/net/sf/picard/analysis/directed/HsMetricsCalculator.java

src/java/net/sf/picard/cmdline/CommandLineParser.java

src/java/net/sf/picard/cmdline/CommandLineProgram.java

src/java/net/sf/picard/cmdline/CreateHtmlDocForProgram.java

src/java/net/sf/picard/cmdline/CreateHtmlDocForStandardOptions.java

src/java/net/sf/picard/cmdline/Option.java

src/java/net/sf/picard/fastq/BamToBfq.java

src/java/net/sf/picard/fastq/BamToBfqWriter.java

src/java/net/sf/picard/io/IoUtil.java

src/java/net/sf/picard/metrics/AggregateMetricCollector.java

src/java/net/sf/picard/metrics/MetricBase.java

src/java/net/sf/picard/metrics/MetricCollector.java

src/java/net/sf/picard/metrics/MetricsFile.java

src/java/net/sf/picard/reference/AbstractFastaSequenceFile.java

src/java/net/sf/picard/reference/ExtractSequences.java

src/java/net/sf/picard/reference/IndexedFastaSequenceFile.java

src/java/net/sf/picard/reference/NormalizeFasta.java

src/java/net/sf/picard/reference/ReferenceSequenceFileFactory.java

src/java/net/sf/picard/sam/AbstractAlignmentMerger.java

src/java/net/sf/picard/sam/AddOrReplaceReadGroups.java

src/java/net/sf/picard/sam/BamIndexStats.java

src/java/net/sf/picard/sam/BuildBamIndex.java

src/java/net/sf/picard/sam/CigarClippingIterator.java

src/java/net/sf/picard/sam/CleanSam.java

src/java/net/sf/picard/sam/CoordinateSortedPairInfoMap.java

src/java/net/sf/picard/sam/DiskReadEndsMap.java

src/java/net/sf/picard/sam/DuplicationMetrics.java

src/java/net/sf/picard/sam/FastqToSam.java

src/java/net/sf/picard/sam/FixMateInformation.java

src/java/net/sf/picard/sam/MarkDuplicates.java

src/java/net/sf/picard/sam/MergeBamAlignment.java

src/java/net/sf/picard/sam/MergeSamFiles.java

src/java/net/sf/picard/sam/MergingSamRecordIterator.java

src/java/net/sf/picard/sam/ReorderSam.java

src/java/net/sf/picard/sam/ReservedTagConstants.java

src/java/net/sf/picard/sam/RevertSam.java

src/java/net/sf/picard/sam/SamAlignmentMerger.java

src/java/net/sf/picard/sam/SamFileValidator.java

src/java/net/sf/picard/sam/SamFormatConverter.java

src/java/net/sf/picard/sam/SamPairUtil.java

src/java/net/sf/picard/sam/SamToFastq.java

src/java/net/sf/picard/sam/ValidateSamFile.java

src/java/net/sf/picard/util/BaiToText.java

src/java/net/sf/picard/util/BamIndexStats.java

src/java/net/sf/picard/util/BuildBamIndex.java

src/java/net/sf/picard/util/CigarUtil.java

src/java/net/sf/picard/util/CollectionUtil.java

src/java/net/sf/picard/util/FileAppendStreamLRUCache.java

src/java/net/sf/picard/util/FormatUtil.java

src/java/net/sf/picard/util/Histogram.java

src/java/net/sf/picard/util/Interval.java

src/java/net/sf/picard/util/IntervalList.java

src/java/net/sf/picard/util/IntervalTreeMap.java

src/java/net/sf/picard/util/Log.java

src/java/net/sf/picard/util/ResourceLimitedMapFunctor.java

src/java/net/sf/picard/util/SamRecordIntervalIteratorFactory.java

src/java/net/sf/samtools/AbstractBAMFileIndex.java

src/java/net/sf/samtools/AbstractBAMIndexWriter.java

src/java/net/sf/samtools/AbstractSAMHeaderRecord.java

src/java/net/sf/samtools/BAMFileReader.java

src/java/net/sf/samtools/BAMFileWriter.java

src/java/net/sf/samtools/BAMIndex.java

src/java/net/sf/samtools/BAMIndexBuilder.java

src/java/net/sf/samtools/BAMIndexContent.java

src/java/net/sf/samtools/BAMIndexMetaData.java

src/java/net/sf/samtools/BAMIndexWriter.java

src/java/net/sf/samtools/BAMIndexer.java

src/java/net/sf/samtools/BAMRecord.java

src/java/net/sf/samtools/BAMRecordCodec.java

src/java/net/sf/samtools/BamIndexValidator.java

src/java/net/sf/samtools/BamIndexerForExistingBai.java

src/java/net/sf/samtools/Bin.java

src/java/net/sf/samtools/BinaryBAMIndexWriter.java

src/java/net/sf/samtools/BinaryTagCodec.java

src/java/net/sf/samtools/BrowseableBAMIndex.java

src/java/net/sf/samtools/CachingBAMFileIndex.java

src/java/net/sf/samtools/Chunk.java

src/java/net/sf/samtools/Cigar.java

src/java/net/sf/samtools/DiskBasedBAMFileIndex.java

src/java/net/sf/samtools/LinearIndex.java

src/java/net/sf/samtools/SAMBinaryTagAndValue.java

src/java/net/sf/samtools/SAMFileHeader.java

src/java/net/sf/samtools/SAMFileReader.java

src/java/net/sf/samtools/SAMFileSpan.java

src/java/net/sf/samtools/SAMFileWriterFactory.java

src/java/net/sf/samtools/SAMProgramRecord.java

src/java/net/sf/samtools/SAMReadGroupRecord.java

src/java/net/sf/samtools/SAMRecord.java

src/java/net/sf/samtools/SAMRecordCoordinateComparator.java

src/java/net/sf/samtools/SAMRecordQueryNameComparator.java

src/java/net/sf/samtools/SAMSequenceRecord.java

src/java/net/sf/samtools/SAMTextHeaderCodec.java

src/java/net/sf/samtools/SAMTextWriter.java

src/java/net/sf/samtools/SAMValidationError.java

src/java/net/sf/samtools/TextualBAMIndexWriter.java

src/java/net/sf/samtools/util/BlockCompressedFilePointerUtil.java

src/java/net/sf/samtools/util/BlockCompressedInputStream.java

src/java/net/sf/samtools/util/BlockCompressedOutputStream.java

src/java/net/sf/samtools/util/IOUtil.java

src/java/net/sf/samtools/util/Md5CalculatingInputStream.java

src/java/net/sf/samtools/util/Md5CalculatingOutputStream.java

src/java/net/sf/samtools/util/SeekableBufferedStream.java

src/java/net/sf/samtools/util/SeekableHTTPStream.java

src/java/net/sf/samtools/util/SequenceUtil.java

src/java/net/sf/samtools/util/StringUtil.java

src/scripts/release_picard.sh

src/tests/java/net/sf/picard/analysis/CollectAlignmentSummaryMetricsTest.java

src/tests/java/net/sf/picard/cmdline/CommandLineParserTest.java

src/tests/java/net/sf/picard/reference/IndexedFastaSequenceFileTest.java

src/tests/java/net/sf/picard/sam/FastqToSamTest.java

src/tests/java/net/sf/picard/sam/MergeBamAlignmentTest.java

src/tests/java/net/sf/picard/sam/SamFileHeaderMergerTest.java

src/tests/java/net/sf/picard/sam/SamToFastqTest.java

src/tests/java/net/sf/picard/sam/ValidateSamFileTest.java

src/tests/java/net/sf/picard/util/CigarUtilTest.java

src/tests/java/net/sf/picard/util/HistogramTest.java

src/tests/java/net/sf/picard/util/IOUtilTest.java

src/tests/java/net/sf/samtools/BAMFileIndexTest.java

src/tests/java/net/sf/samtools/BAMIndexWriterTest.java

src/tests/java/net/sf/samtools/BinTest.java

src/tests/java/net/sf/samtools/ChunkTest.java

src/tests/java/net/sf/samtools/CigarTest.java

src/tests/java/net/sf/samtools/SAMFileReaderTest.java

src/tests/java/net/sf/samtools/SAMFileWriterFactoryTest.java

src/tests/java/net/sf/samtools/SAMTextReaderTest.java

src/tests/java/net/sf/samtools/SAMTextWriterTest.java

src/tests/java/net/sf/samtools/util/BlockCompressedFilePointerUtilTest.java

src/tests/java/net/sf/samtools/util/SequenceUtilTest.java

src/tests/java/net/sf/samtools/util/SortingCollectionTest.java

src/tests/java/net/sf/samtools/util/SortingLongCollectionTest.java

testdata/net/sf/picard/sam/MergeBamAlignment/

testdata/net/sf/picard/sam/MergeBamAlignment/aligned.badorder.sam

testdata/net/sf/picard/sam/MergeBamAlignment/allread1.trimmed.aligned.sam

testdata/net/sf/picard/sam/MergeBamAlignment/allread2.trimmed.aligned.sam

testdata/net/sf/picard/sam/MergeBamAlignment/firsthalf.read1.trimmed.aligned.sam

testdata/net/sf/picard/sam/MergeBamAlignment/firsthalf.read2.trimmed.aligned.sam

testdata/net/sf/picard/sam/MergeBamAlignment/multihit.aligned.sam

testdata/net/sf/picard/sam/MergeBamAlignment/multihit.unmapped.sam

testdata/net/sf/picard/sam/MergeBamAlignment/secondhalf.read1.trimmed.aligned.sam

testdata/net/sf/picard/sam/MergeBamAlignment/secondhalf.read2.trimmed.aligned.sam

testdata/net/sf/picard/sam/MergeBamAlignment/unmapped.badorder.sam

testdata/net/sf/picard/sam/MergeBamAlignment/unmapped.sam

testdata/net/sf/picard/sam/ValidateSamFileTest/bad_index.bai

testdata/net/sf/picard/sam/ValidateSamFileTest/bad_index.bam

testdata/net/sf/picard/sam/bam2fastq/paired/bad/grouped-unpaired-mate.sam

testdata/net/sf/picard/sam/bam2fastq/paired/ok/grouped-last-pair-mates-flipped.sam

testdata/net/sf/picard/sam/onehalfaligned.sam

testdata/net/sf/picard/sam/otherhalfaligned.sam

testdata/net/sf/picard/sam/summary_alignment_stats_test2.sam

testdata/net/sf/samtools/BAMFileIndexTest/test_human.bai

testdata/net/sf/samtools/block_compressed.sam.gz

testdata/net/sf/samtools/compressed.bam

testdata/net/sf/samtools/compressed.sam.gz

testdata/net/sf/samtools/uncompressed.sam

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