Mauricio Carneiro 0e93cf5297 Taking care of bad cigars in the GATK ... * fixed BadCigarFilter to filter out reads starting/ending in deletion and that have adjacent I/D events. * added Unit tests for BadCigarFilter * updated all exceptions in LocusIteratorByState to tell the user that he can instead run with -rf BadCigar * added the BadCigar filter to ReduceReads and RealignTargetCreator (if your walker blows up with these malformed reads, you may want to add it too)		2012-03-20 14:32:57 -04:00
..
R	GATKReport v1.0	2012-03-12 23:09:19 -04:00
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	Taking care of bad cigars in the GATK	2012-03-20 14:32:57 -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	Merge branch 'master' of ssh://gsa1.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable	2012-03-13 09:28:16 -04:00
testdata	adding on-the-fly recalibration test data	2012-03-16 13:18:16 -04:00