Mauricio Carneiro 74344a3871 Bringing in the changes from the CMI repo		2012-12-13 21:59:37 -05:00
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bqsr	Updating tests to handle bad validation data files (that used the wrong qual score encoding); overrides push from stable.	2012-12-03 22:01:07 -05:00
compression/reducereads	Added integration test to catch the read off contig in ReduceReads.	2012-12-12 13:49:54 -05:00
genotyper	Actual working version of unflushing VCFWriter	2012-12-13 16:15:08 -05:00
haplotypecaller	Related bug fixes to GGA mode in the HC: some variants (especially MNPs) were causing problems because they don't have to start at the current location to match the allele being genotyped. Fixed.	2012-12-10 14:47:04 -05:00