gatk3的最后一个经典版本3.8

aaron 831d430025 Added a collection for storing GenomeLocs, that also has functions for removing by genomic region (that may span multiple GenomeLoc's in the collection), and adding regions, which are then merged with any overlapping regions. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@809 348d0f76-0448-11de-a6fe-93d51630548a		2009-05-22 21:52:40 +00:00
c	Move non-java code out of playground.	2009-03-23 19:31:38 +00:00
doc	Added documentation for calling the GATK from Matlab. This is to document the extreme basic and experimental support for using Matlab to call the GATK, and is more of a placeholder for when we have time to revisit supporting this.	2009-05-13 15:25:51 +00:00
java	Added a collection for storing GenomeLocs, that also has functions for removing by genomic region (that may span multiple GenomeLoc's in the collection), and adding regions, which are then merged with any overlapping regions.	2009-05-22 21:52:40 +00:00
python	Better version of MergeBAMBatch -- more options for creating the file	2009-05-21 22:26:19 +00:00
settings	Upped sam-jdk jar to new version in public picard repository.	2009-05-17 15:03:05 +00:00
shell	Move non-java code out of playground.	2009-03-23 19:31:38 +00:00
testdata	Better interface to the tabular ROD, now makes writing files easier. Also has corresponding test files	2009-05-14 23:20:11 +00:00
build.xml	We now only build the files that have changed. It should speed up compile time as our source tree grows.	2009-05-15 20:48:01 +00:00
ivy.xml	remove the ivy command for dependency on BCEL, we're not using it right now.	2009-05-21 19:35:53 +00:00