Mark DePristo 5894d045cb Bugfixes and code cleanup throughout so BCF2 passes VC -> BCF -> VC tests ... -- This version of BCF should actually work properly for most files, assuming headers are properly defined. -- Lots of bug fixes to BCF2 codec -- Genotype getPhredScaledQual is now an int, returning -1 if there's no QUAL. NOTE THIS SEMANTICS change -- Equals() method for GenotypeLikelihoods, using PLs. -- VCFCodec now longer adds empty bindings to missing input field values. NOTE THIS CHANGE -- VCs can be marked as fully decoded, so that when fullyDecode() is called it returns itself, instead of doing the decoding work. The BCF2 codec now makes VCs marked as fully decoded -- stringToBytes returns empty list for null or "" string in BCF2Encoder -- Proper handling of genotype ordering in BCF2 reader / writer -- Removed the crazy slow noDups and sameSamples tests that were slowing down unit and integration tests totally unnecessarily -- Many failing MD5s now due to double -> int change in GQ, will update later		2012-05-27 11:17:17 -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	Yet More missing md5's	2012-05-25 17:21:47 -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	Bugfixes and code cleanup throughout so BCF2 passes VC -> BCF -> VC tests	2012-05-27 11:17:17 -04:00
BaseTest.java	Bugfixes and code cleanup throughout so BCF2 passes VC -> BCF -> VC tests	2012-05-27 11:17:17 -04:00
MD5DB.java	Even more conservative limit on number of differences to summarize at 1000	2012-05-27 11:17:13 -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	Bugfixes and code cleanup throughout so BCF2 passes VC -> BCF -> VC tests	2012-05-27 11:17:17 -04:00