gatk3的最后一个经典版本3.8

Eric Banks 8e2094d2af Updated AssessReducedQuals and applied it systematically to all ReduceReads integration tests. ... * Moved to protected for packaging purposes. * Cleaned up and removed debugging output. * Fixed logic for epsilons so that we really only test significant differences between BAMs. * Other small fixes (e.g. don't include low quality reduced reads in overall qual). * Most RR integration tests now automatically run the quals test on output. * A few are disabled because we expect them to fail in various locations (e.g. due to downsampling).		2013-03-31 00:27:14 -04:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	Updated AssessReducedQuals and applied it systematically to all ReduceReads integration tests.	2013-03-31 00:27:14 -04:00
public	Big bad bug fix: feature added to LeftAlignAndTrimVariants to left align multiallelic records didn't work.	2013-03-30 19:31:28 -04:00
settings	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
.gitignore	Fixing the licensing scripts	2013-01-26 13:42:49 -05:00
build.xml	Fix tests that were consistently or intermittently failing when run in parallel on the farm	2013-03-06 13:56:54 -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	Brought all of ReduceReads to fastutils	2013-02-23 22:53:23 -05:00