Eric Banks b4749757f8 Fixes for SLOD: 1) didn't work properly for multi-allelics (randomly chose an allele, possibly one that wasn't genotyped in the full context); 2) in cases when there were more alt alleles than the max allowed and the user is calculating SB, we would recompute the best alt alleles(s); 3) for some reason, we were recomputing the LOD for the full context when we'd already done that. Given that this passes integration tests on my end, this should be the last commit before the release.		2012-03-12 01:07:07 -04:00
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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	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
doc	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
java	Fixes for SLOD: 1) didn't work properly for multi-allelics (randomly chose an allele, possibly one that wasn't genotyped in the full context); 2) in cases when there were more alt alleles than the max allowed and the user is calculating SB, we would recompute the best alt alleles(s); 3) for some reason, we were recomputing the LOD for the full context when we'd already done that. Given that this passes integration tests on my end, this should be the last commit before the release.	2012-03-12 01:07:07 -04:00
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	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
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