gatk-3.8

gatk3的最后一个经典版本3.8

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kshakir 80259b9e20 Changed fullCallingPipeline to output all contigs in the refence if scattering. When the cleaner interval scatter count is set to one explicitly setting the intrevals to Nil. TODO: Need to add an option that lets the user choose from the command line to scatter all contigs or just those in the intervals list. For now can get relatively the same behavior by setting the interval scatter count equal to the number of contigs+1, assuming the random contigs come at the end of the sequence dictionary. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4565 348d0f76-0448-11de-a6fe-93d51630548a		2010-10-24 03:01:06 +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	Retire old ROD syntax.	2010-10-22 23:52:11 +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	Changed fullCallingPipeline to output all contigs in the refence if scattering.	2010-10-24 03:01:06 +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