gatk3的最后一个经典版本3.8

Mark DePristo 53a904bcbd Bugfix for HaplotypeCaller: GSA-822 for trimming softclipped reads ... -- Previous version would not trim down soft clip bases that extend beyond the active region, causing the assembly graph to go haywire. The new code explicitly reverts soft clips to M bases with the ever useful ReadClipper, and then trims. Note this isn't a 100% fix for the issue, as it's possible that the newly unclipped bases might in reality extend beyond the active region, should their true alignment include a deletion in the reference. Needs to be fixed. JIRA added -- See https://jira.broadinstitute.org/browse/GSA-822 -- #resolve #fix GSA-822		2013-03-20 22:54:36 -04:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	Bugfix for HaplotypeCaller: GSA-822 for trimming softclipped reads	2013-03-20 22:54:36 -04:00
public	HaplotypeCaller now has the ability to only consider the best N haplotypes for genotyping	2013-03-20 22:54:36 -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