Ryan Poplin ca96544ed0 All the zero quality N bases in the solid reads are adding lots of extra paths in the assembly graph. We now require a minimum base quality for every base in the kmer before adding it to the graph. The large number of solid reads with unmapped mates was also triggering the active region traversal at every base. We now ignore that check for solid reads.		2012-03-29 16:14:29 -04:00
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R	Further cleanup of R	2012-03-22 21:24:37 -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	All the zero quality N bases in the solid reads are adding lots of extra paths in the assembly graph. We now require a minimum base quality for every base in the kmer before adding it to the graph. The large number of solid reads with unmapped mates was also triggering the active region traversal at every base. We now ignore that check for solid reads.	2012-03-29 16:14:29 -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	Added more primitives to GATK Report Column Type	2012-03-28 09:07:54 -04:00
testdata	BQSR Gatherer implementation and integration tests	2012-03-27 13:50:22 -05:00