gatk3的最后一个经典版本3.8

delangel cf9c9ae241 Three important updates for Dindel genotyper: ... a) Fix it up because it broke with a recent checkin to annotate vcf with unfiltered depth. b) Printout of ref/alt alleles in output vcf was incorrect because the start/stop positions of associated GenomeLoc were incorrectly computed in case of a deletion. c) Redid Beagle input/output walkers as not assume that ref was a single base, not to assume that variant was a vcf and generalized it to be indel-capable, so now the Beagle walkers can be used for indels as well. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4541 348d0f76-0448-11de-a6fe-93d51630548a		2010-10-21 16:00:16 +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	Three important updates for Dindel genotyper:	2010-10-21 16:00:16 +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	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	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	- 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
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