Christopher Hartl 365f1d2429 hmk123's error on the forum came from the reference context occasionally lacking bases needed for validating the reference bases in the variant context. (no @Window for VariantsToBinaryPed). This bugfix adresses this and other minor items: ... 1) ValidateVariants removed in favor of direct validation VariantContexts. Integration test added to test broken contexts. 2) Enabling indel and SV output. Still bi-allelic sites only. Integration tests added for these cases. 3) Found a bug where GQ recalculation (if a genotype has PLs but no GQ) would only happen for flipped encoding. Fixed. Integration test added.		2012-09-29 00:55:31 -04:00
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R	Fix for missing formatter in R 2.15	2012-08-17 11:49:02 -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	…
java	hmk123's error on the forum came from the reference context occasionally lacking bases needed for validating the reference bases in the variant context. (no @Window for VariantsToBinaryPed). This bugfix adresses this and other minor items:	2012-09-29 00:55:31 -04:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	Removed 'Walker' suffix from packages/GATKEngine.xml that were breaking the packaged release.	2012-07-23 16:32:31 -04:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Bugfix for potential SEGFAULT with JNA getting execution hosts for LSF with multiple hosts	2012-08-17 11:49:01 -04:00
testdata	Reverting move of BQSR tests to public, as per DR's email	2012-07-19 10:02:05 -04:00