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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 f3dacd3c40 Use ByteBuffer.allocateDirect() instead of ByteBuffer.allocate(). 
ByteBuffer.allocateDirect() behaves like Java NIO MappedByteBuffers in that
it consumes address space, which counts against our virtual memory allocation;
but cannot be destroyed or otherwise freed.  This was definitely contributing
to the LSF failures that I was seeing, but I'm not yet convinced that it's the
sole source of these virtual memory 'leaks'.  More tomorrow as the results of
my whole exome tests start to roll in.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5693 348d0f76-0448-11de-a6fe-93d51630548a
 		2011-04-27 02:01:11 +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 Missing file from last checkin. 2011-04-26 00:12:41 +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