David Roazen 3b2fab9a37 Update stable for shptmp -> hptmp migration		2012-06-05 17:38:06 -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	Don't compute QD if there is no QUAL; added integration test for this	2012-05-03 11:02:37 -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	disabling all BQSR unit tests	2012-04-30 14:39:55 -04:00
BaseTest.java	Update stable for shptmp -> hptmp migration	2012-06-05 17:38:06 -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	New way to handle exceptions in multi-threaded GATK	2012-04-13 09:23:33 -04:00