Mauricio Carneiro d379c3763a DNA Sequence to BitSet and vice-versa conversion tools ... * Turns DNA sequences (for context covariates) into bit sets for maximum compression * Allows variable context size representation guaranteeing uniqueness. * Works with long precision, so it is limited to a context size of 31 bases (can be extended with BigNumber precision if necessary). * Unit Tests added		2012-02-29 19:25:20 -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	Another test where we no longer print out 'NaN' for the AF.	2012-02-27 15:19:08 -05:00
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	DNA Sequence to BitSet and vice-versa conversion tools	2012-02-29 19:25:20 -05:00
BaseTest.java	Refactor the Pileup Element with regards to indels	2012-01-24 16:07:21 -05:00
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