gatk3的最后一个经典版本3.8

Mark DePristo 83fcc06e28 LIBS optimizations and performance tools ... -- Made LIBSPerformance a full featured CommandLineProgram, and it can be used to assess the LIBS performance by reading a provided BAM -- ReadStateManager now provides a clean interface to iterate in sample order the per-sample read states, allowing us to avoid many map.get calls -- Moved updateReadStates to ReadStateManager -- Removed the unnecessary wrapping of an iterator in ReadStateManager -- readStatesBySample is now a LinkedHashMap so that iteration occurs in LIBS sample order, allowing us to avoid many unnecessary calls to map.get iterating over samples. Now those are just map native iterations -- Restructured collectPendingReads for simplicity, removing redundant and consolidating common range checks. The new piece is code is much clearer and avoids several unnecessary function calls		2013-01-14 16:30:15 -05:00
licensing	Cleaning CRLF terminations in the licenses	2013-01-10 17:06:29 -05:00
protected/java	Merge branch 'master' of gsa2:/humgen/gsa-scr1/chartl/dev/unstable	2013-01-14 13:27:34 -05:00
public	LIBS optimizations and performance tools	2013-01-14 16:30:15 -05:00
settings	Final r119 tribble jar	2012-11-02 14:30:33 -04:00
.gitignore	adding some directories to gitignore	2012-09-27 11:09:41 -04:00
build.xml	Updating Queue maven version to 0.0.2	2013-01-10 13:46:49 -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	ReadBackedPileup cleanup	2013-01-11 15:17:18 -05:00