Eric Banks 6253ba164e Using --keepOriginalAC in SelectVariants was causing it to emit bad VCFs ... * This occurred when one or more alleles were lost from the record after selection * Discussed here: http://gatkforums.broadinstitute.org/discussion/comment/4718#Comment_4718 * Added some integration tests for --keepOriginalAC (there were none before)		2013-04-05 00:53:28 -04:00
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R	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
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doc	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
java	Using --keepOriginalAC in SelectVariants was causing it to emit bad VCFs	2013-04-05 00:53:28 -04:00
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	Split out contig names from Reference .fai file on white space (to support the GATK resource bundle's file human_g1k_v37.fasta.fai.gz, which does not use tab delimiters)	2012-06-07 16:56:32 -04:00
scala	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
testdata	Reverting move of BQSR tests to public, as per DR's email	2012-07-19 10:02:05 -04:00