Roger Zurawicki 0e9c2cefa2 testHardClipSoftClippedBases works with Matches and Deletions ... Insertions are a problem so cigar cases with "I" are commented out. The test works with multiple deletions and matches. This is still not a complete test. A lot of cigar test cases are commented out. Added insertions to ReadClipperUnitTest ReadClipper now tests for all indels. Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>		2011-12-09 11:43:37 -05:00
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R	scales=free shows variance within analysis better	2011-12-07 14:09:32 -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	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	testHardClipSoftClippedBases works with Matches and Deletions	2011-12-09 11:43:37 -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	Use optional() instead of required() to construct javaMemoryLimit argument in JavaCommandLineFunction	2011-12-05 14:06:00 -05:00
testdata	Testdata for IntervalStratification	2011-11-10 11:08:34 -05:00