gatk3的最后一个经典版本3.8

kshakir 7f25019f37 Inprocess functions by default now log what output files they are running for. ... On -run cleaning up .done and .fail files for jobs that will be run. Added detection to Firehose YAML generator shell script for (g)awk versions that ignore "\n" in patterns. Removed obsolete mergeText and splitIntervals shell scripts. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4452 348d0f76-0448-11de-a6fe-93d51630548a		2010-10-07 19:08:02 +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	Removed the qScale arguments in VariantRecalibrator. It is smarter about how it tries to find a cut so the arbitrary scale factor hopefully is no longer necessary. Now the recalibrated variant quality score more accurately reflects our believed lod of the call.	2010-10-07 18:04:57 +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	/broad/1KG doesn't exist	2010-10-06 12:54:38 +00:00
perl	update the example: /broad/1KG doesn't exist anymore	2010-10-05 13:50:24 +00:00
python	File reports are now sorted in order	2010-10-06 21:54:23 +00:00
ruby	accidentally commited an old tool	2010-08-25 15:42:02 +00:00
scala	Inprocess functions by default now log what output files they are running for.	2010-10-07 19:08:02 +00:00
settings	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
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	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