Eric Banks 26e71f6688 The Omni files have multiple records (with the same ALT) at a particular location, with one PASSing and the other(s) filtered. Chris, this is why using this file as both eval and comp leads to ref/no-call cells in the GenotypeConcordance table. However, this led to non-determinism in VE because the VCs were placed in a HashSet; we use a LinkedHashMap instead to bring back determinism.		2011-09-27 11:03:17 -04:00
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R	Merge branch 'master' into sgintervals	2011-09-19 09:50:19 -04:00
c	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
chainFiles	…
doc	…
java	The Omni files have multiple records (with the same ALT) at a particular location, with one PASSing and the other(s) filtered. Chris, this is why using this file as both eval and comp leads to ref/no-call cells in the GenotypeConcordance table. However, this led to non-determinism in VE because the VCs were placed in a HashSet; we use a LinkedHashMap instead to bring back determinism.	2011-09-27 11:03:17 -04:00
packages	Changing packaging system path for GATK-only Tribble codecs.	2011-09-26 14:58:19 -04:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Merge branch 'master' of ssh://gsa3.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable	2011-09-27 00:51:45 -04:00
testdata	Adding bgzip vcf file for unit tests	2011-09-21 15:39:45 -04:00