Eric Banks b6a1967f12 Better documentation for ValidateVariants so that people realize it's used for strict validation of the VCF file. Added an option to turn off strict validation and an integration test to cover it.		2012-10-29 21:47:09 -04:00
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commandline	Refactored argument matching to support other plugins in addition to file lists.	2012-10-15 15:10:45 -04:00
gatk	Better documentation for ValidateVariants so that people realize it's used for strict validation of the VCF file. Added an option to turn off strict validation and an integration test to cover it.	2012-10-29 21:47:09 -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	Fix some of the broken integration tests	2012-10-26 11:23:44 -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	Renaming -cnt to -nct for consistency	2012-09-05 21:13:19 -04:00