Eric Banks f7c2c818fe Exact model memory optimization: instead of having a later matrix column pull in data from earlier ones (requiring us to keep them around until all dependencies are hit), the earlier columns push data into their dependents immediately and then are removed. This does trade off speed a little bit (because we need to call approximateLog10Sum each time we add to a dependent instead of once in an array at the end). Note that this commit would normally not get pushed into stable, but I'm about to make a very disruptive push into stable that would make merging this from unstable a nightmare.		2012-03-14 14:02:36 -04:00
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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	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	Exact model memory optimization: instead of having a later matrix column pull in data from earlier ones (requiring us to keep them around until all dependencies are hit), the earlier columns push data into their dependents immediately and then are removed. This does trade off speed a little bit (because we need to call approximateLog10Sum each time we add to a dependent instead of once in an array at the end). Note that this commit would normally not get pushed into stable, but I'm about to make a very disruptive push into stable that would make merging this from unstable a nightmare.	2012-03-14 14:02:36 -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	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