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gatk-3.8/java/src/net/sf/samtools
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hanna dc885ba386 Fix for some correctness bugs found during early performance testing, phase 1. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2822 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-02-10 22:32:25 +00:00
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BAMBlockIterator.java Updates to chunk iteration. Includes the return of the dreaded *2.java files; 2010-01-08 20:20:56 +00:00
BAMChunkIterator.java First successful test of new sharding system prototype. Can traverse over reads from a single 2010-01-15 03:35:55 +00:00
BAMFileHeaderLoader.java First successful test of new sharding system prototype. Can traverse over reads from a single 2010-01-15 03:35:55 +00:00
BAMFileIndex2.java Basic use cases for merging BAM files with the new sharding system work. 2010-02-09 22:14:37 +00:00
BAMFileReader2.java Fix for some correctness bugs found during early performance testing, phase 1. 2010-02-10 22:32:25 +00:00
Bin.java Basic use cases for merging BAM files with the new sharding system work. 2010-02-09 22:14:37 +00:00
Block.java A rethink of the existing BAM block extraction code: rather than working in 2009-12-30 18:19:51 +00:00
BlockReader.java A rethink of the existing BAM block extraction code: rather than working in 2009-12-30 18:19:51 +00:00
BlockSegment.java First successful test of new sharding system prototype. Can traverse over reads from a single 2010-01-15 03:35:55 +00:00
BlockTestHarness.java Updates to chunk iteration. Includes the return of the dreaded *2.java files; 2010-01-08 20:20:56 +00:00
Chunk.java Add an alternate implementation of the BAM file reader that keeps the entire index in memory. Initial revision of BAMFileStat, a tool to inspect BAM file BGZF blocks and index entries. 2010-02-03 19:48:15 +00:00
LinearIndex.java Add an alternate implementation of the BAM file reader that keeps the entire index in memory. Initial revision of BAMFileStat, a tool to inspect BAM file BGZF blocks and index entries. 2010-02-03 19:48:15 +00:00
SAMFileReader2.java Supporting infrastructure for merging SAM files. Not yet integrated into the datasource. 2010-02-08 23:59:38 +00:00