gatk3的最后一个经典版本3.8

Mark DePristo d9cdc5d006 Optimization: track alleles in the PerReadAlleleLikelihoodMap with a HashSet ... -- The previous version of PerReadAlleleLikelihoodMap only stored the alleles in an ArrayList, and used ArrayList.contains() to determine if an allele was already present in the map. This is very slow with many alleles. Now keeps both the ArrayList (for get() performance) and a Set of alleles for contains().		2013-05-21 16:18:56 -04:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	Base Recalibrator doesn't recalibrate all reads, so the final output line was confusing	2013-05-21 11:35:05 -04:00
public	Optimization: track alleles in the PerReadAlleleLikelihoodMap with a HashSet	2013-05-21 16:18:56 -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