gatk3的最后一个经典版本3.8

chartl a56a2dfdb7 Nothing to see here. Move along. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5681 348d0f76-0448-11de-a6fe-93d51630548a		2011-04-22 15:01:02 +00:00
R	Moved scripts to phasing/scripts sub-directory	2011-04-11 15:25:39 +00:00
analysis/depristo	Scripts for creating S3 IGV account	2011-04-02 13:39:47 +00:00
archive	Moving GLF code to archive	2011-01-15 22:42:42 +00:00
c	Bug fixes for the bwa aligner and changes to support compiling against newer releases of the bwa code base.	2010-12-17 14:49:15 +00:00
chainFiles	Adding chain files for Mark. Tested by lifting over back and forth between builds. Note that they comprise only the standard contigs so no _randoms or GL000xxx.1s.	2011-04-22 14:53:15 +00:00
doc	removing the custom reflections library from the libs, and adding a release version. Hopefully this will fix the problem Menachem has been seeing with random JVM crashes. Also	2010-08-19 00:42:37 +00:00
java	Nothing to see here. Move along.	2011-04-22 15:01:02 +00:00
lua	forgot to remove a debug line.	2011-02-15 16:25:48 +00:00
matlab	Another matlab script -- this time for making power and coverage plots over a specific gene region. Lots of fun file reading, string manipulation, and exploration of the set() function	2009-11-30 20:02:25 +00:00
packages	Another case of just because you can do something doesn't mean you should.	2011-04-15 15:39:56 +00:00
perl	Quit immediately with an error message if any of the individual steps fails.	2011-04-22 13:23:33 +00:00
python	A helper script that will take a list of bams, a list of case sample IDs, and a list of control sample IDs, and generate a sample meta data yaml (which includes the bamfiles)	2011-03-21 16:11:55 +00:00
ruby	accidentally commited an old tool	2010-08-25 15:42:02 +00:00
scala	Queue graph time is currently of O(n^m) where n = num jobs, m = num unique base files. This script therefore was running in order 1200^16, which I don't think would finish before the heat death of the universe. For now, push down the number of files to 1 and gather them outside of Queue, once I've fixed up scatter-gather in core, outputs can be uncommented.	2011-04-21 12:56:25 +00:00
settings	Revved Picard to access new flag to disable mmap for bam indices. Only added a 3% speed boost but the mmap was added to the heap count, making it harder to specify/restrict the total resident memory size in LSF. Specifying -Xmx4g will now stay much closer to 4g resident memory usage versus bumping up to 9g when accessing 900 x ~8Mb bai's.	2011-04-01 01:40:41 +00:00
shell	Useful utility for looking at the file size of GSA file systems	2011-04-02 03:47:27 +00:00
testdata	ReplaceReadGroups. Fixes BAM files without read group info. MissingReadGroup points people to this tool now. Please point users on the forum to this tool now. Will migrate to Picard.	2011-02-21 14:02:41 +00:00
LICENSE	Adding a license to the root directory in case BOSC checks for one. Has the	2010-04-20 16:04:29 +00:00
build.xml	Marked boolean SAMFileWriterATD arguments as flags so scala generator maps them to Boolean instead of Option[Boolean].	2011-04-08 18:44:32 +00:00
ivy.xml	Added commons math, for Kristian.	2011-02-14 18:57:21 +00:00