Mauricio Carneiro 7cf9911924 Fixed ReduceReads bug where variant regions were missing. ... This affected variant regions with more than 100 reads and less than 250 reads. Only bams reduced with GATK v2 and 2.1 were affected.		2012-09-19 16:09:08 -04:00
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bqsr	Temporarily disabling multi-threaded usage of BaseRecalibrator for performance reasons.	2012-08-20 12:43:17 -04:00
compression/reducereads	Fixed ReduceReads bug where variant regions were missing.	2012-09-19 16:09:08 -04:00
genotyper	Fix for performance problem in GGA mode related to previous --regenotype commit. Instead of trying to hack around the determination of the calculation model when it's not needed, just simply overload the calculateGenotypes() method to add one that does simple genotyping. Re-enabling the Pool Caller integration tests.	2012-08-16 13:05:17 -04:00
haplotypecaller	Bug fix for popular _Duplicate allele added to VariantContext_ error reported on the forum. It seems to be due to lower case bases in the reference being treated as reference mismatches. We would try to turn these mismatches into SNP events, for example c/C. We now uppercase the result from IndexedFastaSequenceFile.getSubsequenceAt()	2012-08-22 14:39:35 -04:00