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gatk3的最后一个经典版本3.8
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257 MiB
Java 95.8%
Scala 3.8%
R 0.2%
JavaScript 0.1%
 
 
 
 
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kshakir 6b1b4931e7 Added FCP VE stratifications for Filter, FunctionalClass, and Stratification as requested by Corin. 
Feeding FCP UG the bam list instead of individual bams to cut scatter gather time from O(m^100) as measured by Chris to O(m^1).
Fixed NPE when eval values aren't found in PipelineTests.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5694 348d0f76-0448-11de-a6fe-93d51630548a
 		2011-04-27 02:29:56 +00:00
R Moved scripts to phasing/scripts sub-directory 2011-04-11 15:25:39 +00:00
analysis/depristo Scripts for creating S3 IGV account 2011-04-02 13:39:47 +00:00
archive Moving GLF code to archive 2011-01-15 22:42:42 +00:00
c Bug fixes for the bwa aligner and changes to support compiling against newer releases of the bwa code base. 2010-12-17 14:49:15 +00:00
chainFiles Adding chain files for Mark. Tested by lifting over back and forth between builds. Note that they comprise only the standard contigs so no _randoms or GL000xxx.1s. 2011-04-22 14:53:15 +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 Use ByteBuffer.allocateDirect() instead of ByteBuffer.allocate(). 2011-04-27 02:01:11 +00:00
lua forgot to remove a debug line. 2011-02-15 16:25:48 +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 Added JavaMail dependencies to Queue package since bcel wasn't picking them up. 2011-04-23 20:48:40 +00:00
perl Quit immediately with an error message if any of the individual steps fails. 2011-04-22 13:23:33 +00:00
python A helper script that will take a list of bams, a list of case sample IDs, and a list of control sample IDs, and generate a sample meta data yaml (which includes the bamfiles) 2011-03-21 16:11:55 +00:00
ruby accidentally commited an old tool 2010-08-25 15:42:02 +00:00
scala Added FCP VE stratifications for Filter, FunctionalClass, and Stratification as requested by Corin. 2011-04-27 02:29:56 +00:00
settings Ported small BAM performance test suite to the Google Caliper microbenchmarking suite. Looks promising, 2011-04-22 22:09:17 +00:00
shell Useful utility for looking at the file size of GSA file systems 2011-04-02 03:47:27 +00:00
testdata ReplaceReadGroups. Fixes BAM files without read group info. MissingReadGroup points people to this tool now. Please point users on the forum to this tool now. Will migrate to Picard. 2011-02-21 14:02:41 +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 Marked boolean SAMFileWriterATD arguments as flags so scala generator maps them to Boolean instead of Option[Boolean]. 2011-04-08 18:44:32 +00:00
ivy.xml Updating to apache commons math v2. 2011-04-26 17:31:49 +00:00