Ryan Poplin c6ded4d23c Bug fix for hard clipping reads when base insertion and base deletion qualities are present in the read. Updating HaplotypeCaller integration tests to reflect all the recent changes.		2012-03-05 17:54:42 -05:00
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R	Now converts gatkreports to properly typed R data types in gsa.read.gatkreport	2012-03-02 09:11:59 -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 for hard clipping reads when base insertion and base deletion qualities are present in the read. Updating HaplotypeCaller integration tests to reflect all the recent changes.	2012-03-05 17:54:42 -05:00
packages	Revved Picard to incorporate tfennell's AsyncSAMFileWriter.	2011-12-06 10:37:42 -05:00
perl	…
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