Guillermo del Angel 63b1e737c6 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable		2012-04-03 15:43:50 -04:00
..
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	Removing extended event related unit tests	2012-04-02 14:40:36 -04:00
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	Forgot to add tolerance to new MathUtils unit tests	2012-03-28 08:18:36 -04:00
BaseTest.java	Major refactor/completion of new Pool Caller under UnifiedGenotyper framework. PoolAFCalculationModel implements new math to combine pools - correct, but still O(N^2) and not complete yet for multiallelics. Pool likelihoods are better encapsulated and kept in an internal hashmap from int[] -> double for space efficiency (likelihoods can be big for pool calls when in initial discovery mode with 4 alleles). Maybe need several iterations of optimization to make it runnable at large scale. Still need to correct function chooseMostLikelyAlternateAlleles before full runs can be produced.	2012-04-03 15:43:32 -04:00
MD5DB.java	Merged bug fix from Stable into Unstable	2011-10-13 18:02:06 -04:00
MedianUnitTest.java	Adding more unit tests and contracts to PairHMM util class. Updating HaplotypeCaller to use the new PairHMM util class. Now that the HMM result isn't dependent on the length of the haplotype there is no reason to ensure all haplotypes have the save length which simplifies the code considerably.	2012-03-05 08:28:42 -05:00
StingTextReporter.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
WalkerTest.java	Minor: cleaner way of turning off index-on-the-fly checking in case we want to turn it back on.	2012-03-18 00:53:29 -04:00