Mark DePristo cda8d944b7 Bugfixes for BCF with VQSR ... -- Old version converted doubles directly from strings. New version uses VariantContext getAttributeAsDouble() that looks at the values directly to determine how to convert from Object to Double (via Double.valueOf, (Double), or (Double)(Integer)). -- getAttributeAsDouble() is now smart in converting integers to doubles as needed -- Removed unnecessary logging info in BCF2Codec -- Added integration tests to ensure that VQSR works end-to-end with BCF2 using sites version of the file khalid sent to me -- Added vqsr.bcf_test.snps.unfiltered.bcf file for this integration test		2012-08-07 17:22:39 -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	Cleanup of VCF header lines and constants, BCF2 bugfixes	2012-06-21 15:16:31 -04:00
gatk	Bugfixes for BCF with VQSR	2012-08-07 17:22:39 -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	Deleting empty unit test for AdaptiveContexts	2012-08-06 12:58:13 -04:00
BaseTest.java	Extensive unit tests, contacts, and documentation for RecalDatum	2012-07-31 08:11:03 -04:00
MD5DB.java	Finalizing BCF2 mark III commit	2012-06-21 15:16:27 -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	On the way to really sorting out HMS error handling	2012-07-25 22:11:10 -04:00