asivache 9666d47d17 ooops, debug print now removed ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3550 348d0f76-0448-11de-a6fe-93d51630548a		2010-06-14 18:07:12 +00:00
..
IndelGenotyperV2Walker.java	Restructuring of ReferenceContext and ReadWalkers to accept a ReferenceContext. Now ReferenceContext is byte[] backed not char[]. Please no more chars for the reference. All of the tests pass now. Coming check-ins are going to clean up the char / byte problems in the GATK	2010-05-19 23:27:55 +00:00
IndelRealigner.java	ooops, debug print now removed	2010-06-14 18:07:12 +00:00
RealignerTargetCreator.java	Removing more toUpperCase sanity checks	2010-06-02 14:38:39 +00:00
SAMRecordCoordinateComparatorWithUnmappedReads.java	We were still dropping halves of some pairs, in which both reads were assigned to the same position. Fixed.	2010-02-24 23:13:23 +00:00
SortingSAMFileWriter.java	1. Added functionality to the data sources to allow engine to get mapping from input files to (merged) read group ids from those files.	2010-02-04 04:12:49 +00:00