gatk-3.8

gatk3的最后一个经典版本3.8

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kshakir 88a0d77433 Changed parsing engine to store the order the argument bindings based on their definition in the class, moving "-T" to the front of Queue command lines. Queue GATK generated .intervals is now a List(File) again removing special case handling in the generator. Instead of using @Scatter annotation, using ScatterFunction instance to determine if a job can be scattered. Implemented special VcfGatherFunction which only uses the header from the first file, even if the other files differ in their headers. Added a -deleteIntermediates to Queue to delete the outputs from intermediate commands after a successful run. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4536 348d0f76-0448-11de-a6fe-93d51630548a		2010-10-20 21:43:52 +00:00
R	Better reporting -- figured out how to drop unused levels in subset	2010-10-06 14:31:51 +00:00
archive	Cleaning up playground utils and tests	2010-08-27 01:25:47 +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	Changed parsing engine to store the order the argument bindings based on their definition in the class, moving "-T" to the front of Queue command lines.	2010-10-20 21:43:52 +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	Patch for James	2010-10-20 02:39:16 +00:00
python	Adding a script to do big table conversion. Removing Ben's script which is totally obsolete and busted.	2010-10-12 01:40:43 +00:00
ruby	accidentally commited an old tool	2010-08-25 15:42:02 +00:00
scala	Changed parsing engine to store the order the argument bindings based on their definition in the class, moving "-T" to the front of Queue command lines.	2010-10-20 21:43:52 +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	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