Eric Banks ff180a8e02 Significant refactoring of the Haplotype Caller to handle problems with GGA. The main fix is that we now maintain a mapping from 'original' allele to 'Smith-Waterman-based' allele so that we no longer need to do a (buggy) matching throughout the calling process.		2012-11-19 09:09:57 -05:00
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bqsr	Adding integration test to BQSR for the csv file	2012-11-09 09:11:04 -05:00
compression/reducereads	Co-Reduction implementation in ReduceReads	2012-11-14 10:33:21 -05:00
genotyper	Updating integration tests	2012-11-06 22:23:05 -08:00
haplotypecaller	Significant refactoring of the Haplotype Caller to handle problems with GGA. The main fix is that we now maintain a mapping from 'original' allele to 'Smith-Waterman-based' allele so that we no longer need to do a (buggy) matching throughout the calling process.	2012-11-19 09:09:57 -05:00