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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R	Protect ourselves when iteration is present but there's only a single iteration in queueJobReport.R	2011-12-19 10:08:38 -05:00
c	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
chainFiles	…
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java	Added REVERT_SOFTCLIPPED_BASES capability to ReadClipper	2011-12-20 00:04:30 -05:00
packages	Revved Picard to incorporate tfennell's AsyncSAMFileWriter.	2011-12-06 10:37:42 -05:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Removing cruft that snuck in last commit.	2011-12-16 23:00:16 -05:00
testdata	Data Processing Pipeline Test	2011-12-12 00:24:51 -05:00