Eric Banks 11a71e0390 RR bug: when determining the most common base at a position, break ties by which base has the highest sum of base qualities. Otherwise, sites with 1 Q2 N and 1 Q30 C are ending up as Ns in the consensus. I think perhaps we don't even care about which base has the most observations - it should just be determined by which has the highest sum of base qualities - but I'm not sure that's what users would expect.		2012-09-24 21:46:14 -04:00
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src/org/broadinstitute/sting	RR bug: when determining the most common base at a position, break ties by which base has the highest sum of base qualities. Otherwise, sites with 1 Q2 N and 1 Q30 C are ending up as Ns in the consensus. I think perhaps we don't even care about which base has the most observations - it should just be determined by which has the highest sum of base qualities - but I'm not sure that's what users would expect.	2012-09-24 21:46:14 -04:00
test/org/broadinstitute/sting/gatk/walkers	Turn off RR tests while I debug	2012-09-21 17:26:00 -04:00