Eric Banks c54e84e739 Ryan confirmed that we don't need separate arguments to control the context size for insertions and deletions, which allows us to cut down the expensive context calculations.		2012-06-15 09:28:56 -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	Nearing final BCF commit	2012-06-14 16:42:32 -04:00
gatk	Ryan confirmed that we don't need separate arguments to control the context size for insertions and deletions, which allows us to cut down the expensive context calculations.	2012-06-15 09:28:56 -04:00
jna	Updated hard limit MathUtils.MAXN number of samples from 11,000 to 50,000.	2012-05-29 11:18:22 -04:00
utils	Final cleanup of VCFWriterUnitTest	2012-06-14 16:42:39 -04:00
BaseTest.java	Fix bug in incorrectly reporting relative paths in log	2012-06-14 16:42:37 -04:00
MD5DB.java	Algorithmically faster version of DiffEngine	2012-06-14 16:42:30 -04:00
MD5Mismatch.java	Final updates to integration tests for BCF2	2012-05-24 10:58:59 -04:00
StingTextReporter.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
WalkerTest.java	Initial version of clean, fast formatting routines built dynamically from a VCF header	2012-06-14 16:42:30 -04:00