gatk3的最后一个经典版本3.8

Guillermo del Angel 8fbf9c947f Upgrades and changes to LeftAlignVariants, motivated by 1000G consensus indel production: ... -- Added ability to trim common bases in front of indels before left-aligning. Otherwise, records may not be left-aligned if they have common bases, as they will be mistaken by complext records. -- Added ability to split multiallelic records and then left align them, otherwise we miss a lot of good left-aligneable indels. -- Motivated by this, renamed walker to LeftAlignAndTrimVariants. -- Code refactoring, cleanup and bring up to latest coding standards. -- Added unit testing to make sure left alignment is performed correctly for all offsets. -- Changed phase 3 HC script to new syntax. Add command line options, more memory and reduce alt alleles because jobs keep crashing.		2013-03-29 10:02:06 -04:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	Upgrades and changes to LeftAlignVariants, motivated by 1000G consensus indel production:	2013-03-29 10:02:06 -04:00
public	Upgrades and changes to LeftAlignVariants, motivated by 1000G consensus indel production:	2013-03-29 10:02:06 -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