Christopher Hartl 1be8a88909 Changes: ... 1) GATKArgumentCollection has a command to turn off randomization if setting the seed isn't enough. Right now it's only hooked into RankSumTest. 2) RankSumTest now can be passed a boolean telling it whether to use a dithering or non-randomizing comparator. Unit tested. 3) VariantsToBinaryPed can now output in both individual-major and SNP-major mode. Integration test. 4) Updates to PlinkBed-handling python scripts and utilities. 5) Tool for calculating (LD-corrected) GRMs put under version control. This is analysis for T2D, but I don't want to lose it should something happen to my computer.		2012-10-03 16:02:42 -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	Changes:	2012-10-03 16:02:42 -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	Fixing the VariantContextUtilsUnitTest	2012-09-22 23:24:55 -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