gatk-3.8

gatk3的最后一个经典版本3.8

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asivache f2ee5dc319 regexp fixed, now can find OBS_COUNTS followed by both [C/A/R] (obsolete) and [C/A/T] (current) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4675 348d0f76-0448-11de-a6fe-93d51630548a		2010-11-15 15:28:38 +00:00
R	New version of cutting routines for VQSR. Old code removed. Working unit tests. Best practice with testng integration test (everyone look at it). Walker test now allows you to not specify no. input files, if it can infer input counts from MD5s	2010-11-13 16:19:56 +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	Finally, the logic is right	2010-11-15 14:02:09 +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 the codecs into the RMD indexer that are available in the GATK, not just Tribble	2010-11-11 06:35:04 +00:00
perl	regexp fixed, now can find OBS_COUNTS followed by both [C/A/R] (obsolete) and [C/A/T] (current)	2010-11-15 15:28:38 +00:00
python	V1 of the data processing paper, produced results for the manuscript we presented. Commit for archival purposes	2010-11-11 01:43:21 +00:00
ruby	accidentally commited an old tool	2010-08-25 15:42:02 +00:00
scala	Now actually checking in the integration test mentioned in the prior commit: compiles the full calling pipeline.	2010-11-14 04:27:10 +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	correct test data	2010-11-13 22:17:38 +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	Explicitly set TestNG to run headless with no UI.	2010-11-12 22:02:02 +00:00
ivy.xml	Updated PluginManager so that during testing Queue can dynamically compile and load separately multiple class directories into the same class loader.	2010-11-12 20:14:28 +00:00