Mauricio Carneiro 94791a2a75 Add support for reads starting with insertion ... * Modified cleanCigarShift to allow insertions in the beginning and end of the read * Allowed cigars starting/ending in insertions in the systematic ReadClipper tests * Updated all ReadClipper unit tests * ReduceReads does not hard clip leading insertions by default anymore * SlidingWindow adjusts start location if read starts with insertion * SlidingWindow creates an empty element with insertions to the right * Fixed all potential divide by zero with totalCount() (from BaseCounts) * Updated all Integration tests * Added new integration test for multiple interval reducing		2012-01-03 09:29:45 -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	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	Add support for reads starting with insertion	2012-01-03 09:29:45 -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	Updating the MD5s	2011-12-21 15:14:05 -05:00
testdata	Data Processing Pipeline Test	2011-12-12 00:24:51 -05:00