Eric Banks 39c73a6cf5 1. Ryan and I noticed that the FisherStrand annotation was completely busted for indels with reduced reads; fixed. ... 2. While making the previous fix and unifying FS for SNPs and indels, I noticed that FS was slightly broken in the general case for indels too; fixed. 3. I also fixed a minor bug in the Allele Biased Downsampling code for reduced reads.		2013-01-18 03:35:48 -05:00
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annotator	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
beagle	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
bqsr	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
compression/reducereads	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
diagnostics	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
diffengine	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
fasta	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
filters	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
genotyper	1. Ryan and I noticed that the FisherStrand annotation was completely busted for indels with reduced reads; fixed.	2013-01-18 03:35:48 -05:00
haplotypecaller	1. Ryan and I noticed that the FisherStrand annotation was completely busted for indels with reduced reads; fixed.	2013-01-18 03:35:48 -05:00
indels	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
phasing	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
validation	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
varianteval	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
variantrecalibration	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
variantutils	The CachingIndexedFastaSequenceFile now automatically converts IUPAC bases to Ns and errors out on other non-standard bases.	2013-01-16 10:22:43 -05:00