gatk3的最后一个经典版本3.8

Mark DePristo 7eea6b8f92 ReservoirDownsampler optimizations ... -- Add an option to not allocate always ArrayLists of targetSampleSize, but rather the previous size + MARGIN. This helps for LIBS as most of the time we don't need nearly so much space as we allow -- consumeFinalizedItems returns an empty list if the reservior is empty, which it often true for our BAM files with low coverage -- Allow empty sample lists for SamplePartitioner as these are used by the RefTraversals and other non-read based traversals Make the reservoir downsampler use a linked list, rather than a fixed sized array list, in the expectFewOverflows case		2013-01-14 16:30:16 -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	ReservoirDownsampler optimizations	2013-01-14 16:30:16 -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