Eric Banks 6bee6a1b53 Change the behavior of SelectVariants for PL/AD when it encounters a record that has lost one or more alternate alleles. ... Previously, we would strip out the PLs and AD values since they were no longer accurate. However, this is not ideal because then that information is just lost and 1) users complain on the forum and post it as a bug and 2) it gives us problems in both the current and future (single sample) calling pipelines because we subset samples/alleles all the time and lose info. Now the PLs and AD get correctly selected down. While I was in there I also refactored some related code in subsetDiploidAlleles(). There were no real changes there - I just broke it out into smaller chunks as per our best practices. Added unit tests and updated integration tests. Addressed reviews.		2013-12-03 09:23:03 -05:00
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R	Something changed with the ggtitle syntax in the latest version of ggplot2.	2013-08-14 14:40:03 -04:00
c	At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings.	2012-01-17 14:47:53 -05:00
chainFiles	…
doc	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
java	Change the behavior of SelectVariants for PL/AD when it encounters a record that has lost one or more alternate alleles.	2013-12-03 09:23:03 -05:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	ValidatingPileup was renamed to CheckPileup	2013-02-15 11:56:19 -05:00
perl	Fixing the liftover script to not require strict VCF header validation.	2013-11-07 09:02:17 -05:00
scala	Patched Queue extensions lacking a main class definition	2013-11-22 14:57:09 -05:00
testdata	Walker to create a fastq file from an interval list	2013-06-29 11:24:16 -04:00