gatk3的最后一个经典版本3.8

hanna fece2167b3 Prototype implementation of protoshard merging when protoshard n and protoshard ... n+1 completely overlap. Gives a small but consistent performance increase in non-intervaled whole exome traversals (2.79min original, 2.69min revised). Needs a more in depth analysis of optimal shard sizing to determine a true optimum. Also renamed a variable because Khalid disapproved of my naming choices. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5595 348d0f76-0448-11de-a6fe-93d51630548a		2011-04-08 02:09:14 +00:00
R	Misc changes	2011-02-26 15:35:49 +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
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	Prototype implementation of protoshard merging when protoshard n and protoshard	2011-04-08 02:09:14 +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	Fixed inclusion of GATKEngine into the Queue package.	2011-04-01 17:45:46 +00:00
perl	2 more scripts I found helpful in syncing (and cleaning up) the 1000G mirror	2011-02-22 04:17:36 +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	This is now running. Expect results in a few weeks when the ~7k jobs have percolated through the week queue. Pray gsa1 doesn't go down.	2011-04-07 21:12:59 +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	Modified the buildfile and help extractor doclet so that help text is only	2011-04-07 18:40:53 +00:00
ivy.xml	Added commons math, for Kristian.	2011-02-14 18:57:21 +00:00