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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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hanna 2f8057bf24 Cleanup for multithreading memory leak during integration tests...unregister MXBean at end 
of traversal to avoid holding a reference to the microscheduler, which holds a reference to
the engine, which in turn holds a reference to the walker, which itself holds a reference to
all the data aggregated during the course of the traversal.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4594 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-10-28 18:37:42 +00:00
R Takes a list of BAMs, looks up the read group information in the sequencing platform's SQUID database, and computes the tearsheet stats. Also takes the VariantEval output (R format) and outputs the variant stats and some plots for the tearsheet. This script requires the gsalib library to be in the R library path (add the line '.libPaths('/path/to/Sting/R/')' to your ~/.Rprofile). 2010-10-27 19:06:22 +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 Cleanup for multithreading memory leak during integration tests...unregister MXBean at end 2010-10-28 18:37:42 +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 Commenting out annoying print statement 2010-10-24 11:55:26 +00:00
ruby accidentally commited an old tool 2010-08-25 15:42:02 +00:00
scala Now that the user is required to set the java temp directory, it is safer for the LsfJobRunner to write to the java temp directory instead of the command directory. 2010-10-28 15:00:21 +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 Cleanup for multithreading memory leak during integration tests...unregister MXBean at end 2010-10-28 18:37:42 +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