Mark DePristo 51a3b6e25e No more makePrecisionFormatStringFromDenominatorValue ... -- As values in VCs are becoming their native Java types the VCFWriter needs to own proper float formating. -- Created a smart float formatter in VCFWriter, with unit tests -- Removed makePrecisionFormatStringFromDenominatorValue and its uses -- Fix broken contracted -- Refactored some code from the encoder to utils in BCF2 -- HaplotypeCaller's GenotypingEngine was using old version of subset to context. Replaced with a faster call that I think is correct. Ryan, please confirm.		2012-06-14 16:42:30 -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	No more makePrecisionFormatStringFromDenominatorValue	2012-06-14 16:42:30 -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	No more makePrecisionFormatStringFromDenominatorValue	2012-06-14 16:42:30 -04:00
BaseTest.java	Updated hard limit MathUtils.MAXN number of samples from 11,000 to 50,000.	2012-05-29 11:18:22 -04:00
MD5DB.java	MD5DB for integrationtest management now writes out a md5mismatches files for clean analysis	2012-06-14 16:42:27 -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	MD5DB for integrationtest management now writes out a md5mismatches files for clean analysis	2012-06-14 16:42:27 -04:00