gatk3的最后一个经典版本3.8

aaron 05c5659053 This document is now up as content on the wiki, so I'm removing it from svn. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1140 348d0f76-0448-11de-a6fe-93d51630548a		2009-07-01 15:40:32 +00:00
R	Version 0.2.1 (released) of the TableRecalibrator	2009-06-25 22:50:55 +00:00
c	Move non-java code out of playground.	2009-03-23 19:31:38 +00:00
doc	This document is now up as content on the wiki, so I'm removing it from svn.	2009-07-01 15:40:32 +00:00
java	Don't cry wolf: only one warning is now emitted, instead of tons of warnings.	2009-07-01 13:50:37 +00:00
packages	First step in replacing the Hello, World! document. Revamped the HelloWalker and checked it into the source tree, created a special build file for it, and added it to the packaging tool.	2009-06-30 21:59:54 +00:00
perl	checking in new folder for perl scripts AND a simple script that takes an input text file and reference dictionary (.fai) and performs stable sort of the input lines according to the contig order specified by the dictionary. Position of the contig filed to sort on in the input lines is specified as --k POS option. Input lines may specify contigs that are not in the dictionary, in this case the additional contigs will be added at the end of the sorted output, after all known contigs. The sorting order between these additional contigs is simply the order in which they first appear in the input	2009-05-27 16:34:55 +00:00
python	Version 0.2.1 (released) of the TableRecalibrator	2009-06-25 22:50:55 +00:00
settings	Updates to picard public / private and sam.	2009-06-30 14:50:55 +00:00
shell	Version 0.2.1 (released) of the TableRecalibrator	2009-06-25 22:50:55 +00:00
testdata	Apprach v2. Added python analysis script, so java no longer must be used to analyses quality score data. About to refactor out lots of unneeded code	2009-06-20 16:00:23 +00:00
build.xml	Convert the somatic coverage tool to output from the packaging tool rather than from the dist target.	2009-06-18 21:29:30 +00:00
ivy.xml	Add bcel and cleanup.	2009-06-17 19:28:04 +00:00