Guillermo del Angel 279dff9f81 Bug fix when specifying a JEXL expression for a field that doesn't exist: we should treat the whole expression as false, but we were rethrowing the JEXL exception in this case. Added integration test to cover this in SelectVariants		2012-07-10 13:59:00 -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	Bug fix when specifying a JEXL expression for a field that doesn't exist: we should treat the whole expression as false, but we were rethrowing the JEXL exception in this case. Added integration test to cover this in SelectVariants	2012-07-10 13:59:00 -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	Updates to VCF processing for better BCF processing	2012-07-08 15:44:33 -07:00
BaseTest.java	BCF2 with support symbolic alleles	2012-06-30 11:22:48 -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	Disable shadowBCF for VariantRecalibrationWalkers tests because it cannot handle symbolic alleles yet	2012-06-26 15:28:32 -04:00