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gatk3的最后一个经典版本3.8
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Java 95.8%
Scala 3.8%
R 0.2%
JavaScript 0.1%
 
 
 
 
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kshakir db47230dd9 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. 
Shell invoking scripts so that even really long shell scripts make it through LSF.
Using the truncated (up to 1000 characters) of the command line for the job name for use with bjobs.
Switched the default from re-running everything to re-running only files that need to be regenerated.  --skip_up_to_date replaced with --start_clean for those who want to regenerate everything.
Updated logging to let users know when the scatter gather generator is running, which still takes a while but is orders of magnatudes faster for large lists of functions.  (40s for a 100 function graph exploding to a 2500 function graph)


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4448 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-10-07 01:19:18 +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 Added integration tests for ReadBackedPhasing 2010-10-06 20:50:32 +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 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
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 minor improvements to queue status 2010-10-06 14:34:35 +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