asivache 5202d959bf NM attribute changed in sam jdk (?) from Integer to Short, or maybe it is presented differently by the reader depending on whether SAM or BAM is processed; in any case, both Integer and Short are safe now ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1522 348d0f76-0448-11de-a6fe-93d51630548a		2009-09-03 19:03:32 +00:00
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bwa	Checkpoint. The BWT that we generate now matches the first 16% of the BWT that BWT-SW generates. Cleaned up output streams to separate the byte packing / word packing from the data structure generation.	2009-09-02 22:18:17 +00:00
gatk	VariantFiltration moved to core.	2009-09-03 15:41:41 +00:00
playground	NM attribute changed in sam jdk (?) from Integer to Short, or maybe it is presented differently by the reader depending on whether SAM or BAM is processed; in any case, both Integer and Short are safe now	2009-09-03 19:03:32 +00:00
secondarybase	Cleanup...deprecate FastaSequenceFile2 in favor of IndexedFastaSequenceFile or ReferenceSequenceFile from Picard, depending on the application.	2009-07-08 18:49:08 +00:00
utils	Improvements to make this work with uncompressed fastq files. Pulled the fastq parser out into it's own SAMFileReader-like entity.	2009-09-03 17:20:16 +00:00