gatk3的最后一个经典版本3.8

Mark DePristo 464e65ea96 Disable error correcting kmers by default in the HC ... -- The error correction algorithm can break the reference graph in some cases by error correcting us into a bad state for the reference sequence. Because we know that the error correction algorithm isn't ideal, and worse, doesn't actually seem to improve the calling itself on chr20, I've simply disabled error correction by default and allowed it to be turned on with a hidden argument. -- In the process I've changed a bit the assembly interface, moving some common arguments us into the LocalAssemblyEngine, which are turned on/off via setter methods. -- Went through the updated arguments in the HC to be @Hidden and @Advanced as appropriate -- Don't write out an errorcorrected graph when debugging and error correction isn't enabled		2013-03-26 10:05:17 -04:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	Disable error correcting kmers by default in the HC	2013-03-26 10:05:17 -04:00
public	Added support to reduce reads to Callable Loci	2013-03-21 15:53:04 -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