Mauricio Carneiro 0e93cf5297 Taking care of bad cigars in the GATK ... * fixed BadCigarFilter to filter out reads starting/ending in deletion and that have adjacent I/D events. * added Unit tests for BadCigarFilter * updated all exceptions in LocusIteratorByState to tell the user that he can instead run with -rf BadCigar * added the BadCigar filter to ReduceReads and RealignTargetCreator (if your walker blows up with these malformed reads, you may want to add it too)		2012-03-20 14:32:57 -04:00
..
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	Taking care of bad cigars in the GATK	2012-03-20 14:32:57 -04:00
jna	When using bam list mode in HSP deriving VCF name from bam list instead of requiring an additional parameter.	2011-12-16 18:09:25 -05:00
utils	intermediate commit to aid in debugging HC / exact model changes. HC integration tests will still fail	2012-03-18 15:50:27 -04:00
BaseTest.java	CalibrateGenotypeLikelihoods now emits the position of the variant for debugging	2012-03-09 16:00:07 -05:00
MD5DB.java	Merged bug fix from Stable into Unstable	2011-10-13 18:02:06 -04:00
MedianUnitTest.java	Adding more unit tests and contracts to PairHMM util class. Updating HaplotypeCaller to use the new PairHMM util class. Now that the HMM result isn't dependent on the length of the haplotype there is no reason to ensure all haplotypes have the save length which simplifies the code considerably.	2012-03-05 08:28:42 -05:00
StingTextReporter.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
WalkerTest.java	Minor: cleaner way of turning off index-on-the-fly checking in case we want to turn it back on.	2012-03-18 00:53:29 -04:00