Mauricio Carneiro 5f1afb4136 Fixing an off-by-one clipping error in ReduceReads for reads off the contig ... Reads that are soft-clipped off the contig (before the beginning of the contig) were being soft-clipped to position 0 instead of 1 because of an off-by-one issue. Fixed and included in the integration test.		2012-12-13 22:10:11 -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	Fixing an off-by-one clipping error in ReduceReads for reads off the contig	2012-12-13 22:10:11 -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