gatk3的最后一个经典版本3.8

asivache 2e0296fef9 NWayOut logic slightly changed: 1) results.list file is gone; 2) now with -nWayOut one can specify either a) suffix to attach to every output file (i.e. cleaned reads from inputK.bam will be sent to inputK.suffix.bam) or b) *.map tab-separated file that must list <input_name> <output_name> mappings, one per line, for every input file. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4645 348d0f76-0448-11de-a6fe-93d51630548a		2010-11-10 20:32:16 +00:00
R	now prints a nice report, can be invoked from command line	2010-11-09 19:44:10 +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	NWayOut logic slightly changed: 1) results.list file is gone; 2) now with -nWayOut one can specify either a) suffix to attach to every output file (i.e. cleaned reads from inputK.bam will be sent to inputK.suffix.bam) or b) *.map tab-separated file that must list <input_name> <output_name> mappings, one per line, for every input file.	2010-11-10 20:32:16 +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	by request, an indexer tool to create Tribble style indexes outside of the GATK	2010-11-06 18:59:06 +00:00
perl	Also removed contig intervals from the pipeline sanity check perl scsript.	2010-10-21 11:23:34 +00:00
python	Simple pre-processing script for soapsnp files	2010-11-04 20:34:43 +00:00
ruby	accidentally commited an old tool	2010-08-25 15:42:02 +00:00
scala	Convert GenomeLocParser into an instance variable. This change is required	2010-11-10 17:59:50 +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	GSA-413 Explicitly set all compilers to use 512m memory maximum instead of 64m default maximum and running them out of the ant process.	2010-11-09 19:32:19 +00:00
ivy.xml	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00