gatk3的最后一个经典版本3.8

Mauricio Carneiro ec475a46b1 Fixing @PG tag uniqueness issue ... The Problem: ------------ the SAM spec does not allow multiple @PG tags with the same id. Our @PG tag writing routines were allowing that to happen with the boolean parameter "keep_all_pg_records". How this fixes it: ------------------ This commit removes that option from all the utility functions and cleans up the code around the classes that used these methods off-spec. Summarized changes: ------------------- * Remove keep_all_pg_records option from setupWriter utility methos in Util * Update all walkers to now replace the last @PG tag of the same walker (if it already exists) * Cleanup NWaySamFileWriter now that it doesn't need to keep track of the keep_all_pg_records variable * Simplify the multiple implementations to setupWriter Bamboo: ------- http://gsabamboo.broadinstitute.org/browse/GSAUNSTABLE-PARALLEL31 Issue Tracker: -------------- [fixes 47100885]		2013-03-30 20:31:33 -04:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	Fixing @PG tag uniqueness issue	2013-03-30 20:31:33 -04:00
public	Fixing @PG tag uniqueness issue	2013-03-30 20:31:33 -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