David Roazen 91d10431d3 BAMScheduler: detect contigs from the interval list that are not in the merged BAM header's sequence dictionary ... This is a quick-and-dirty patch for the null pointer error Mauricio reported earlier. Later on we might want to address in a more general way the fact that we validate user intervals against the reference but not against the merged BAM header produced by the engine at runtime.		2012-03-09 15:20:16 -05:00
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R	Now converts gatkreports to properly typed R data types in gsa.read.gatkreport	2012-03-02 09:11:59 -05:00
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	BAMScheduler: detect contigs from the interval list that are not in the merged BAM header's sequence dictionary	2012-03-09 15:20:16 -05:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
perl	…
scala	Mostly small changes to my own scala scripts: .vcf.gz compatibility for output files, smarter beagle generation, simple script to scatter-gather combine variants. Whole genome indel calling now uses the gold standard indel set.	2012-02-22 17:20:04 -05:00
testdata	Added support for breakpoint alleles	2012-02-23 12:14:48 -05:00