gatk3的最后一个经典版本3.8

David Roazen 2a7af43164 Fix improper dependencies in QScripts used by pipeline tests, and attempt to fix the flawed MisencodedBaseQualityUnitTest ... -Some QScripts used by public pipeline tests unnecessarily used the (now protected) UnifiedGenotyper. Changed them to use PrintReads instead. -Moved ExampleUnifiedGenotyperPipelineTest to protected -Attempt to fix the flawed and sporadically failing MisencodedBaseQualityUnitTest: After looking at this class a bit, I think the problem was the use of global arrays for the quals shared across all reads in all tests (BAMRecord class definitely does not make a separate copy for each read!). One test (testFixBadQuals) modifies the bad quals array, and if this happens to run before the testBadQualsThrowsError test the bad quals array will have been "fixed" and no exception will be thrown.		2013-02-27 04:45:53 -05:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	Fix improper dependencies in QScripts used by pipeline tests, and attempt to fix the flawed MisencodedBaseQualityUnitTest	2013-02-27 04:45:53 -05:00
public	Fix improper dependencies in QScripts used by pipeline tests, and attempt to fix the flawed MisencodedBaseQualityUnitTest	2013-02-27 04:45:53 -05:00
settings	Haplotype/Allele based optimizations for the HaplotypeCaller that knock off nearly 20% of the total runtime (multi-sample).	2013-02-21 10:14:11 -05:00
.gitignore	Fixing the licensing scripts	2013-01-26 13:42:49 -05:00
build.xml	Updating TestNG to the latest version	2013-02-22 09:40:23 -05:00
intellij_example.tar.bz2	Removed the intellij files from the root and made an example package for new users. This allows users to start at the same page and then change it as they see fit without interfering with the repo (thanks guillermo!)	2012-09-27 11:04:56 -04:00
ivy.xml	Updating TestNG to the latest version	2013-02-22 09:40:23 -05:00