Guillermo del Angel 5995f01a01 Big intermediate commit (mostly so that I don't have to go again through merge/rebase hell) in expanding BQSR capabilities. Far from done yet: ... a) Add option to stratify CalibrateGenotypeLikelihoods by repeat - will add integration test in next push. b) Simulator to produce BAM files with given error profile - for now only given SNP/indel error rate can be given. A bad context can be specified and if such context is present then error rate is increased to given value. c) Rewrote RepeatLength covariate to do the right thing - not fully working yet, work in progress. d) Additional experimental covariates to log repeat unit and combined repeat unit+length. Needs code refactoring/testing		2013-01-28 19:55:46 -05:00
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net/sf	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
org/broadinstitute	Big intermediate commit (mostly so that I don't have to go again through merge/rebase hell) in expanding BQSR capabilities. Far from done yet:	2013-01-28 19:55:46 -05:00