gatk3的最后一个经典版本3.8

Mauricio Carneiro 403f9de122 Fix another caching issue with the PairHMM ... The Problem ---------- Some read x haplotype pairs were getting very low likelihood when caching is on. Turning it off seemed to give the right result. Solution -------- The HaplotypeCaller only initializes the PairHMM once and then feed it with a set of reads and haplotypes. The PairHMM always caches the matrix when the previous haplotype length is the same as the current one. This is not true when the read has changed. This commit adds another condition to zero the haplotype start index when the read changes. Summarized Changes ------------------ * Added the recacheReadValue check to flush the matrix (hapStartIndex = 0) * Updated related MD5's Bamboo link: http://gsabamboo.broadinstitute.org/browse/GSAUNSTABLE-PARALLEL9		2013-04-12 14:52:45 -04:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	Fix another caching issue with the PairHMM	2013-04-12 14:52:45 -04:00
public	Fix another caching issue with the PairHMM	2013-04-12 14:52:45 -04:00
settings	Don't allow users to specify keys and IDs that contain angle brackets or equals signs (not allowed in VCF spec).	2013-04-05 00:52:32 -04:00
.gitignore	Fixing the licensing scripts	2013-01-26 13:42:49 -05:00
build.xml	Disable Contracts for Java for tests	2013-04-04 11:56:17 -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