Eric Banks f82a7c3f4c Updating variant jar. ... The update contains: 1. documentation changes for VariantContext and Allele (which used to discuss the now obsolete null allele) 2. better error messages for VCFs containing complex rearrangements with breakends 3. instead of failing badly on format field lists with '.'s, just ignore them Also, there is a trivial change to use a more efficient method to remove a bunch of attributes from a VC. Delivers PT#s 59675378, 59496612, and 60524016.		2013-12-31 22:48:29 -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	Updating variant jar.	2013-12-31 22:48:29 -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	Added HC trio calls and NA12878 KB snapshot to resource bundle.	2013-12-07 22:08:34 -05:00
testdata	Walker to create a fastq file from an interval list	2013-06-29 11:24:16 -04:00