Eric Banks 998ed8fff3 Bug fix to deal with VCF records that don't have GTs. While in there, optimized a bunch of related functions (including removing a copy of the method calculateChromosomeCounts(); why did we have 2 copies? very dangerous).		2012-02-27 14:56:10 -05:00
..
R	queueJobReport now compresses PDF when running R 2.13+.	2012-01-10 17:32:30 -05:00
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	…
doc	…
java	Bug fix to deal with VCF records that don't have GTs. While in there, optimized a bunch of related functions (including removing a copy of the method calculateChromosomeCounts(); why did we have 2 copies? very dangerous).	2012-02-27 14:56:10 -05:00
packages	Revved Picard to incorporate tfennell's AsyncSAMFileWriter.	2011-12-06 10:37:42 -05:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Mostly small changes to my own scala scripts: .vcf.gz compatibility for output files, smarter beagle generation, simple script to scatter-gather combine variants. Whole genome indel calling now uses the gold standard indel set.	2012-02-22 17:20:04 -05:00
testdata	Added support for breakpoint alleles	2012-02-23 12:14:48 -05:00