Ryan Poplin 2836c161ee Moving trimToVariableRegion out of reduced reads and into a public static ReadClipper function. HaplotypeCaller clips reads to the active region boundries before passing to the HMM. The philosophy of the HC is moving towards genotyping the entire haplotype sequence contained within the active region as a single allele.		2012-03-11 14:45:59 -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	Moving trimToVariableRegion out of reduced reads and into a public static ReadClipper function. HaplotypeCaller clips reads to the active region boundries before passing to the HMM. The philosophy of the HC is moving towards genotyping the entire haplotype sequence contained within the active region as a single allele.	2012-03-11 14:45:59 -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