Mark DePristo e99ff3caae Removed lots of old, and not to be used, HMM options ... -- resulted in massive code cleanup -- GdA will integrate his new banded algorithm here -- Removed: DO_CONTEXT_DEPENDENT_PENALTIES, GET_GAP_PENALTIES_FROM_DATA, INDEL_RECAL_FILE, dovit, GSA_PRODUCTION_ONLY		2011-09-27 10:08:40 -04:00
..
R	Merge branch 'master' into sgintervals	2011-09-19 09:50:19 -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	…
doc	…
java	Removed lots of old, and not to be used, HMM options	2011-09-27 10:08:40 -04:00
packages	Changing packaging system path for GATK-only Tribble codecs.	2011-09-26 14:58:19 -04:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Merge branch 'master' of ssh://gsa3.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable	2011-09-27 00:51:45 -04:00
testdata	Adding bgzip vcf file for unit tests	2011-09-21 15:39:45 -04:00