David Roazen cb84a6473f Downsampling: experimental engine integration ... -Off by default; engine fork isolates new code paths from old code paths, so no integration tests change yet -Experimental implementation is currently BROKEN due to a serious issue involving file spans. No one can/should use the experimental features until I've patched this issue. -There are temporarily two independent versions of LocusIteratorByState. Anyone changing one version should port the change to the other (if possible), and anyone adding unit tests for one version should add the same unit tests for the other (again, if possible). This situation will hopefully be extremely temporary, and last only until the experimental implementation is proven.		2012-09-06 15:03:27 -04:00
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commandline	- New UserExceptions added for when ReadFilters or Walkers specified on the command line are not found. When -rf xxxx cannot find the class corresponding to xxxx, all read filters are printed in a better formatted way, with links to their gatk docs.	2012-09-04 16:41:44 -04:00
gatk	Downsampling: experimental engine integration	2012-09-06 15:03:27 -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	Downsampling: experimental engine integration	2012-09-06 15:03:27 -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