Ryan Poplin 7a73042cd3 Bug fix for the case of merging two VCs when a deletion deletes the padding base for a consecutive indel. Added unit test to cover this case.		2012-07-30 12:09:23 -04:00
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bqsr	Smoothing in the BQSR bins should be one error observation and one non-error observation.	2012-07-26 13:59:02 -04:00
compression/reducereads	Updating default value for -mindel to the one used by Khalid in the pipeline and me in my tests.	2012-07-10 02:04:26 -04:00
genotyper	Final checkpoint: all tests pass. Note that there were bugs in the PoolGenotypeLikelihoodsUnitTest that needed fixing and eventually led to my needing to disable one of the tests (with a note for Guillermo to look into it). Also note that while I have moved over the GATK to use the new non-null representation of Alleles, I didn't remove all of the now-superfluous code throughout to do padding checking on merges; we'll need to do this on a subsequent push.	2012-07-29 01:07:59 -04:00
haplotypecaller	Bug fix for the case of merging two VCs when a deletion deletes the padding base for a consecutive indel. Added unit test to cover this case.	2012-07-30 12:09:23 -04:00