gatk3的最后一个经典版本3.8

kshakir e9c6f681a4 Instead of the pipeline's cleaner only writing BAMs with the target intervals, now pulling the list of contigs from the target intervals and outputing reads in those contigs. ... Added a brute force -retry <count> option to Queue for transient errors. Waiting up to 2 minutes for the LSF logs to appear before trying to display the errors from the logs. Updates to the local job runner error logging when a job fails. Refactored QGraph's settings as duplicate code was getting out of control. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4563 348d0f76-0448-11de-a6fe-93d51630548a		2010-10-22 22:22:30 +00:00
R	Better reporting -- figured out how to drop unused levels in subset	2010-10-06 14:31:51 +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	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 20:35:44 +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	analyzeRunReports now actually implements no-dev	2010-10-22 19:53:23 +00:00
ruby	accidentally commited an old tool	2010-08-25 15:42:02 +00:00
scala	Instead of the pipeline's cleaner only writing BAMs with the target intervals, now pulling the list of contigs from the target intervals and outputing reads in those contigs.	2010-10-22 22:22:30 +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	Wrapping ScatterGatherableFunctions with a facade instead of using slower clone library. Will require keeping Clone's facade code in sync with CommandLineFunction but runs *much* faster.	2010-10-07 01:19:18 +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