ebanks 849dce799d This rod was all wrong for generating the alternate snp alleles (it returned null or even the wrong value); fixed. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1531 348d0f76-0448-11de-a6fe-93d51630548a		2009-09-04 14:21:46 +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	This rod was all wrong for generating the alternate snp alleles (it returned null or even the wrong value); fixed.	2009-09-04 14:21:46 +00:00
playground	Renaming error to getNegLog10PError(); added Cached clearing method to GL; SSG now has a CallResult that counts calls; No more Adding class to System.out, now to logger.info; First major testing piece (and general approach too) to unit testing of a walker -- SingleSampleGenotyper now knows how many calls to make on a particular 1mb region on NA12878 for each call type and counts the number of calls *AND* the compares the geli MD5 sum to the expected one!	2009-09-04 12:39:06 +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	Renaming error to getNegLog10PError(); added Cached clearing method to GL; SSG now has a CallResult that counts calls; No more Adding class to System.out, now to logger.info; First major testing piece (and general approach too) to unit testing of a walker -- SingleSampleGenotyper now knows how many calls to make on a particular 1mb region on NA12878 for each call type and counts the number of calls *AND* the compares the geli MD5 sum to the expected one!	2009-09-04 12:39:06 +00:00