gatk3的最后一个经典版本3.8

ebanks e6200fe5b5 don't ignore reads when maxReadLength isn't set ... also, print out LOD score for cleaning git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@771 348d0f76-0448-11de-a6fe-93d51630548a		2009-05-21 19:24:10 +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	don't ignore reads when maxReadLength isn't set	2009-05-21 19:24:10 +00:00
python	Slightly improved interface to merging utility for multiple bam files	2009-05-20 12:54:41 +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	add javassist, which is a less lower level version of bcel.	2009-05-20 05:11:03 +00:00