gatk3的最后一个经典版本3.8

Eric Banks a5a68c09fa Fix for the "Removed too many insertions, header is now negative" bug in ReduceReads. ... The problem ultimately was that ReadUtils.readStartsWithInsertion() ignores leading hard/softclips, but ReduceReads does not. So I refactored that method to include a boolean argument as to whether or not clips should be ignored. Also rebased so that return type is no longer a Pair. Added unit test to cover this situation.		2013-05-29 16:41:01 -04:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	Fix for the "Removed too many insertions, header is now negative" bug in ReduceReads.	2013-05-29 16:41:01 -04:00
public	Fix for the "Removed too many insertions, header is now negative" bug in ReduceReads.	2013-05-29 16:41:01 -04:00
settings	Rev picard, sam-jdk, tribble, and variant to version 1.91.1453	2013-05-07 14:21:15 -04:00
.gitignore	Detect stuck lock-acquisition calls, and disable file locking for tests	2013-04-24 22:49:02 -04:00
build.xml	Enable convenient display of diff engine output in Bamboo, plus misc. minor test-related improvements	2013-05-10 19:00:33 -04:00
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