Eric Banks 0f3af9555b Adding an option to SelectVariants which allows the user to re-genotype through the exact model (if PLs are present) the samples in order to recalculate the QUAL and genotypes. This is really the correct way to select a subset of samples, especially when originally called from low coverage data. Also added integration test to cover this case.		2012-05-01 14:58:06 -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	Added ability to specify arguments in files via -args/--arg_file	2011-10-24 15:58:34 -04:00
gatk	Adding an option to SelectVariants which allows the user to re-genotype through the exact model (if PLs are present) the samples in order to recalculate the QUAL and genotypes. This is really the correct way to select a subset of samples, especially when originally called from low coverage data. Also added integration test to cover this case.	2012-05-01 14:58:06 -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	disabling all BQSR unit tests	2012-04-30 14:39:55 -04:00
BaseTest.java	Bug fix: BaseTest change shouldn't have been committed, first cleanup of SNP pool code (more to follow)	2012-04-03 18:55:52 -04:00
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	…
WalkerTest.java	New way to handle exceptions in multi-threaded GATK	2012-04-13 09:23:33 -04:00