kshakir 213cc00abe Refactored argument matching to support other plugins in addition to file lists. ... Added plugin support for sending Queue status messages. Argument parsing can store subclasses of java.io.File, for example RemoteFile.		2012-10-15 15:10:45 -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	Allowing the GATK to have non-required outputs	2012-10-15 13:49:08 -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	Increasing the precision of MathUtils.approximateLog10SumLog10 from 1E-3 to 1E-4. Genotyper integration tests change as a result. Expanding the unit tests of MathUtils.log10sumLog10.	2012-10-15 13:24:32 -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