Roger Zurawicki 091c7197cd Fixed memory leak and bug with deletions in clipping ... The ClippingOp clip cigar function would run into a endless loop if the parameter were out of the reads range, I stopped the bug. * There is no check to make sure the read coordinate are covered by the read though When Hard clipping to interval, I added a check for deletions. NOTE: method works for NA12878 WEx but needs to be more thoroughly tested/optimized		2011-09-18 19:21:51 -04:00
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R	Bugfix for singleton runs. Now with histograms where possible	2011-09-06 16:54:01 -04:00
c	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
chainFiles	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
doc	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
java	Fixed memory leak and bug with deletions in clipping	2011-09-18 19:21:51 -04:00
packages	Added edu.mit.broad.picard to Queue packaged jar.	2011-07-23 14:40:29 -04:00
perl	Moving these supported perl scripts to public	2011-07-01 17:26:25 -04:00
scala	Allowing multiple dnsnp and indel files in the DPP	2011-09-02 13:38:47 -04:00
testdata	GZIP VCF for testing	2011-08-19 09:05:39 -04:00