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
..
alignment	Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable	2011-07-19 20:25:33 -04:00
analyzecovariates	Forgot that no matter how trivial a change it's a good idea to compile first	2011-10-11 11:18:41 -04:00
commandline	Added ability to specify arguments in files via -args/--arg_file	2011-10-24 15:58:34 -04:00
gatk	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
jna	Updates to JobRunners from the Queue developer community and from running the WholeGenomePipeline:	2011-08-22 15:13:27 -04:00
pipeline	Cleanup of the utils.broad package.	2011-07-01 20:47:03 -04:00
queue	Fixed Queue's tagging of RodBindings.	2011-08-21 02:34:20 -04:00
utils	Embedding gsalib source and queueJobReport R scripts in the dist and package jars.	2011-10-24 15:58:34 -04:00