Guillermo del Angel b559936b7a a)New variant eval stratification module for indel size. b) Next iteration on indel caller runtime optimization: when computing likelihood of each haplotype for a given read, many computations will be redundant since pieces of haplotypes will be common to both REF and ALT haplotypes. So, we keep HMM matrices from one haplotype to the next one and recompute starting at the part where either haplotype is different or GOP/GCP are different.		2011-10-25 09:56:43 -04:00
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R	Embedding gsalib source and queueJobReport R scripts in the dist and package jars.	2011-10-24 15:58:34 -04:00
c	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
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	a)New variant eval stratification module for indel size. b) Next iteration on indel caller runtime optimization: when computing likelihood of each haplotype for a given read, many computations will be redundant since pieces of haplotypes will be common to both REF and ALT haplotypes. So, we keep HMM matrices from one haplotype to the next one and recompute starting at the part where either haplotype is different or GOP/GCP are different.	2011-10-25 09:56:43 -04:00
packages	Embedding gsalib source and queueJobReport R scripts in the dist and package jars.	2011-10-24 15:58:34 -04:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Embedding gsalib source and queueJobReport R scripts in the dist and package jars.	2011-10-24 15:58:34 -04:00
testdata	Oops, forgot the PED test file	2011-10-05 21:09:08 -07:00