Guillermo del Angel 58d4539304 Enabled banded indel computation by default. Reversed logic in input UG argument so that we can still disable it if required. Minor changes to integration tests due to minor differences in GL's and in annotations		2012-01-04 15:28:26 -05:00
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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	Enabled banded indel computation by default. Reversed logic in input UG argument so that we can still disable it if required. Minor changes to integration tests due to minor differences in GL's and in annotations	2012-01-04 15:28:26 -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	Added knuth-shuffle (KS) and randomSubset using KS to MathUtils	2012-01-03 09:29:46 -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