Mauricio Carneiro 78d9bf7196 Added REVERT_SOFTCLIPPED_BASES capability to ReadClipper ... * New ClippingOp REVERT_SOFTCLIPPED_BASES turns soft clipped bases into matches. * Added functionality to clipping op to revert all soft clip bases in a read into matches * Added revertSoftClipBases function to the ReadClipper for public use * Wrote systematic unit tests		2011-12-20 00:04:30 -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	- Corrected bug causing cases where both parents are HET to be accounted twice in the TDT calculation - Adapted TDT Integration test to corrected version of TDT	2011-12-19 10:30:59 -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 REVERT_SOFTCLIPPED_BASES capability to ReadClipper	2011-12-20 00:04:30 -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