Eric Banks 1a45ea5a05 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable		2011-12-29 11:37:15 -05:00
..
alignment	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
commandline	Added ability to specify arguments in files via -args/--arg_file	2011-10-24 15:58:34 -04:00
gatk	A much better way of choosing the alternate allele(s) to genotype in the SNP model of UG: instead of looking at the sum of base qualities (which can and did lead to us over-genotyping esp. when allowing multiple alternate alleles), we look at the likelihoods themselves (free since we are already calculating likelihoods for all 10 genotypes). Now, even if the base quals exceed some arbitrary threshold, we only bother genotyping an alternate allele when there's a sample for which it is more likely than ref/ref (I can generate weird edge cases where this falls apart, but none that model truly variable sites that we actually want to call). This leads to a huge efficiency improvement esp. for exomes (and esp. for many samples) where we almost always were trying to genotype all 3 alternate alleles. Integration tests change only because ref calls have slight QUAL differences (because the best alt allele is still chosen arbitrarily, but differently).	2011-12-27 16:50:38 -05:00
jna	When using bam list mode in HSP deriving VCF name from bam list instead of requiring an additional parameter.	2011-12-16 18:09:25 -05:00
utils	Made all class methods private in the ReadClipper	2011-12-27 02:11:32 -05:00
BaseTest.java	Removing cruft that snuck in last commit.	2011-12-16 23:00:16 -05:00
MD5DB.java	Merged bug fix from Stable into Unstable	2011-10-13 18:02:06 -04:00
StingTextReporter.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
WalkerTest.java	All MD5 mismatches for test are shown	2011-10-04 15:53:52 -07:00