Mauricio Carneiro 17efbbf8b1 Fixed ReadClipperUnitTest ... The behavior of the clipping on weird cigar strings such as 1I1S1H and 9S56H has changed, and the test has to change accordingly.		2012-07-03 16:38:51 -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	Adding the model name to the VQSR filter lines so that they don't get clobbered with consecutive VQSR runs for SNPs and then indels.	2012-07-03 14:30:37 -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	Fixed ReadClipperUnitTest	2012-07-03 16:38:51 -04:00
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