andrewk 5dab95aa5a Fix getMergedReadGroupsByReaders so that it provides read groups in the same way Picard does so that it works correctly when input read files have no clashes in their read groups and retain their original read group names. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1737 348d0f76-0448-11de-a6fe-93d51630548a		2009-09-29 06:35:50 +00:00
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alignment	Add in weights. Massive performance improvements.	2009-09-24 23:19:15 +00:00
gatk	Fix getMergedReadGroupsByReaders so that it provides read groups in the same way Picard does so that it works correctly when input read files have no clashes in their read groups and retain their original read group names.	2009-09-29 06:35:50 +00:00
playground	Cosmetic change to list sampling functions: the typical usage of n and k were reversed. No change in functionality of the classes has been made and unit tests still pass.	2009-09-28 18:12:32 +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	Cosmetic change to list sampling functions: the typical usage of n and k were reversed. No change in functionality of the classes has been made and unit tests still pass.	2009-09-28 18:12:32 +00:00