gatk3的最后一个经典版本3.8

hanna d492621122 The TraversalEngine's habit of hanging onto old ROD states seems to have a bad ... interaction with Tribble. In Tribble, keeping these references in memory until the shard is flushed means keeping one 512K character buffer per object in memory. Fixed by purging the reference to the object at the end of the shard traversal. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4599 348d0f76-0448-11de-a6fe-93d51630548a		2010-10-29 17:09:58 +00:00
R	Takes a list of BAMs, looks up the read group information in the sequencing platform's SQUID database, and computes the tearsheet stats. Also takes the VariantEval output (R format) and outputs the variant stats and some plots for the tearsheet. This script requires the gsalib library to be in the R library path (add the line '.libPaths('/path/to/Sting/R/')' to your ~/.Rprofile).	2010-10-27 19:06:22 +00:00
archive	Fisher exact makes a return. Seems to be working properly. Current tagged as a work in progress. Needs to take the filtered context to be truly correct.	2010-10-22 20:35:53 +00:00
c	Reduce file handle usage.	2010-01-05 18:03:01 +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	The TraversalEngine's habit of hanging onto old ROD states seems to have a bad	2010-10-29 17:09:58 +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	Include all standard annotations	2010-10-11 20:52:08 +00:00
perl	Also removed contig intervals from the pipeline sanity check perl scsript.	2010-10-21 11:23:34 +00:00
python	Commenting out annoying print statement	2010-10-24 11:55:26 +00:00
ruby	accidentally commited an old tool	2010-08-25 15:42:02 +00:00
scala	Now that the user is required to set the java temp directory, it is safer for the LsfJobRunner to write to the java temp directory instead of the command directory.	2010-10-28 15:00:21 +00:00
settings	Added status email support with -statusTo. Will send emails on failure of an individual function or success/failure of the whole pipeline.	2010-10-14 15:58:52 +00:00
shell	Inprocess functions by default now log what output files they are running for.	2010-10-07 19:08:02 +00:00
testdata	Fixes for example bam files	2010-10-05 18:43:02 +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	Cleanup for multithreading memory leak during integration tests...unregister MXBean at end	2010-10-28 18:37:42 +00:00
ivy.xml	- After removing special code for intervals, instead of being of type File they are generated as List[File]. Changed previous checkin that was appending to this list and instead assigning a singleton list.	2010-10-21 06:37:28 +00:00