gatk3的最后一个经典版本3.8

kshakir dee130ad1b Gather the log files before the actual outputs and mark the log files gatherers as intermediates. ... Since the outputs will only be gathered iff the logs were gathered this allows the job name to change without causing SG to re-run. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5285 348d0f76-0448-11de-a6fe-93d51630548a		2011-02-21 22:04:35 +00:00
R	Now says FNR, not FDR. We really need to clean up VQSR	2011-02-15 12:28:09 +00:00
analysis/depristo	Scripts to create the GATK IAM user and give him/her rights to PutObject (and only PutObject) into the S3 storage instance. Updated the GATKRunReport to now upload using the GATK user, not mark@depristo.com. Running with -et AWS_S3 sends run reports up to the Amazon S3 cloud now. Going to request a few external users try this option so we can see it running at scale. I'm sure S3 can handle a few hundred thousand 1Kb uploads per days, though	2011-01-31 03:48:33 +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	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
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	Adding the native jna support libraries from the jna.jar to the Queue package jar.	2011-01-08 10:48:30 +00:00
perl	Checking in the scripts I'm using for syncing the 1000G mirror. Note that very few people can actually use them because you most likely don't have perission to write to /humgen/1kg/DCC, but these should be used as a resource if anyone ever needs to do this in the future. These scripts are very naive and consist of just the actual pulling down of data. Currently aspera and wget are supported, but Mark should feel free to add lftp if he wants. :) Also, while I'm here, I'm removing obsolete scripts for running an obsolete pipeline.	2011-02-20 03:59:26 +00:00
python	Modifications, bugfix to theoretical posteriors. (Bug fix: eliminated discontinuity in prior distribution)	2011-02-14 19:47:34 +00:00
ruby	accidentally commited an old tool	2010-08-25 15:42:02 +00:00
scala	Gather the log files before the actual outputs and mark the log files gatherers as intermediates.	2011-02-21 22:04:35 +00:00
settings	Update Picard / sam-jdk at Tim's request.	2011-01-03 02:17:25 +00:00
shell	Forgot to enable printing	2011-02-19 14:51:33 +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	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
ivy.xml	Added commons math, for Kristian.	2011-02-14 18:57:21 +00:00