Mark DePristo c8a06e53c1 DoC now properly handles reference N bases + misc. additional cleanups ... -- DoC now by default ignores bases with reference Ns, so these are not included in the coverage calculations at any stage. -- Added option --includeRefNSites that will include them in the calculation -- Added integration tests that ensures the per base tables (and so all subsequent calculations) work with and without reference N bases included -- Reorganized command line options, tagging advanced options with @Advanced		2012-02-25 11:32:50 -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	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	DoC now properly handles reference N bases + misc. additional cleanups	2012-02-25 11:32:50 -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