Eric Banks ef87b18e09 In retrospect, it wasn't a good idea to have FisherStrand handle reduced reads since they are always on the forward strand. For now, FS ignores reduced reads but I've added a note (and JIRA) to make this work once the RR het compression is enabled (since we will have directionality in reads then).		2012-12-05 02:00:35 -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	Co-Reduction implementation in ReduceReads	2012-11-14 10:33:21 -05:00
genotyper	In retrospect, it wasn't a good idea to have FisherStrand handle reduced reads since they are always on the forward strand. For now, FS ignores reduced reads but I've added a note (and JIRA) to make this work once the RR het compression is enabled (since we will have directionality in reads then).	2012-12-05 02:00:35 -05:00
haplotypecaller	Updating the HC integration test md5s. According to the NA12878 knowledge base this commit cuts down the FP rate by more than 50 percent with no loss in sensitivity.	2012-12-03 15:38:59 -05:00