Mauricio Carneiro d16cb68539 Updated and more thorough version of the BadCigar read filter ... * No reads with Hard/Soft clips in the middle of the cigar * No reads starting with deletions (with or without preceding clips) * No reads ending in deletions (with or without follow-up clips) * No reads that are fully hard or soft clipped * No reads that have consecutive indels in the cigar (II, DD, ID or DI) Also added systematic test for good cigars and iterative test for bad cigars.		2012-08-17 17:05:27 -04:00
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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	Cleanup of VCF header lines and constants, BCF2 bugfixes	2012-06-21 15:16:31 -04:00
gatk	Updated and more thorough version of the BadCigar read filter	2012-08-17 17:05:27 -04:00
jna	Updated hard limit MathUtils.MAXN number of samples from 11,000 to 50,000.	2012-05-29 11:18:22 -04:00
utils	Updated and more thorough version of the BadCigar read filter	2012-08-17 17:05:27 -04:00
BaseTest.java	Extensive unit tests, contacts, and documentation for RecalDatum	2012-07-31 08:11:03 -04:00
MD5DB.java	Finalizing BCF2 mark III commit	2012-06-21 15:16:27 -04:00
MD5Mismatch.java	Final updates to integration tests for BCF2	2012-05-24 10:58:59 -04:00
StingTextReporter.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
WalkerTest.java	On the way to really sorting out HMS error handling	2012-07-25 22:11:10 -04:00