Mauricio Carneiro d00b2c6599 Adding a synthetic read for filtered data ... * Generalized the concept of a synthetic read to cread both running consensus and a synthetic reads of filtered data. * Synthetic reads can now have deletions (but not insertions) * New reduced read tag for filtered data synthetic reads *(RF)* * Sliding window header now keeps information of consensus and filtered data * Synthetic reads are created simultaneously, new functionality is controlled internally by addToSyntheticReads		2011-11-09 20:16:22 -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	Merged bug fix from Stable into Unstable	2011-11-07 15:26:35 -05:00
jna	Fixed an integration test which crashed on the out of date LSF DRMAA library when run against the obsolete LSF dotkit instead of .combined_LSF_SGE	2011-09-23 21:03:22 -04:00
pipeline	Cleanup of the utils.broad package.	2011-07-01 20:47:03 -04:00
utils	Adding a synthetic read for filtered data	2011-11-09 20:16:22 -05:00
BaseTest.java	merge master	2011-10-25 16:08:39 -04:00
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