Ryan Poplin 98f18b5f9e Changing the HC over to using the non-contamination-downsampled read maps for the purposes of annotations. This behavior now matches the UG. There is a new command line option to go back to the older behavior to explore the differences.		2012-12-17 11:27:44 -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	Changing the HC over to using the non-contamination-downsampled read maps for the purposes of annotations. This behavior now matches the UG. There is a new command line option to go back to the older behavior to explore the differences.	2012-12-17 11:27:44 -05:00