Mark DePristo f77d2e6965 Renamed NO_HEADER to the more accurate no_cmdline_in_header ... -- Also no_cmdline_in_header permits us to write contigs into the header, so that the shadow BCF system can work as well		2012-05-24 10:57:08 -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	Renamed NO_HEADER to the more accurate no_cmdline_in_header	2012-05-24 10:57:08 -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	Renamed NO_HEADER to the more accurate no_cmdline_in_header	2012-05-24 10:57:08 -04:00
BaseTest.java	Testing of BCF codec	2012-05-24 10:57:01 -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	Rev'ing Tribble from 53 to 94	2012-05-03 07:31:47 -04:00