Mark DePristo 2ca5fc62a2 Support for MISSING BCF2 type ... -- Heng wants to use 0x0? to represent any missing type value, which in our implementation was invalid. Updated our codebase to support this construct. Heng said he'll update the BCF2 quick reference. -- Enabled integration test reading Heng's ex2.bcf file -- GATK now only warns in the case where the END info field isn't the same (or +1 due to padding) as the getEnd() function as determined by the GATK. Turns out there's a single record in the 1000G SV call set that doesn't have the right length -- VariantContextTestProvider now tests that X = Y where X -> writing -> reading -> writing -> reading = Y for a variety of variant context inputs X -- Added integration test reading 1000G SV chr1 calls (from Chris)		2012-07-19 16:14:26 -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	Reverting move of BQSR tests to public, as per DR's email	2012-07-19 10:02:05 -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	Support for MISSING BCF2 type	2012-07-19 16:14:26 -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