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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 cc5d695bcf Renamed the IPFL Test to IPFL PipelineTest so that it'll be picked up by the PipelineTests. 
HACK: Turned off JNA autoRead() in the jobInfoEnt LSF structure to try and dodge the SIGSEGV during strlen calls during bmods. 


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5201 348d0f76-0448-11de-a6fe-93d51630548a
 		2011-02-05 00:06:12 +00:00
R Use the yaml as an arguemtn to get out squid numbers 2011-02-03 18:32:05 +00:00
analysis/depristo Scripts to create the GATK IAM user and give him/her rights to PutObject (and only PutObject) into the S3 storage instance. Updated the GATKRunReport to now upload using the GATK user, not mark@depristo.com. Running with -et AWS_S3 sends run reports up to the Amazon S3 cloud now. Going to request a few external users try this option so we can see it running at scale. I'm sure S3 can handle a few hundred thousand 1Kb uploads per days, though 2011-01-31 03:48:33 +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
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 Renamed the IPFL Test to IPFL PipelineTest so that it'll be picked up by the PipelineTests. 2011-02-05 00:06:12 +00:00
lua small bug fix on chromosome names. 2011-02-01 20:55:19 +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 Adding the native jna support libraries from the jna.jar to the Queue package jar. 2011-01-08 10:48:30 +00:00
perl Fixed bug that required users to use the recordOriginalLocation option 2011-01-05 23:12:14 +00:00
python updates to handle only reporting on a specific SVN revision. Updated the R script to show the domain name of the runner, now that S3 logging is working 2011-02-01 12:02:12 +00:00
ruby accidentally commited an old tool 2010-08-25 15:42:02 +00:00
scala Renamed the IPFL Test to IPFL PipelineTest so that it'll be picked up by the PipelineTests. 2011-02-05 00:06:12 +00:00
settings Update Picard / sam-jdk at Tim's request. 2011-01-03 02:17:25 +00:00
shell Calls the bams pulled down from firehose cleaned by default 2011-02-03 18:34:07 +00:00
testdata VQSR now operates on LOD scores in the INFO field directly, and doesn't adjust the QUAL field. New format for tranches file uses LOD score. Old file format no longer supported. log10sumlog10() function, a very useful utility in MathUtils. No more ExtendedPileupElement! Robust math calculations in GMM so that no infinities are generated! HaplotypeScore refactored to enable use of filtered context. Not yet enabled... InferredContext getDouble and getInteger arguments now parse values from Strings if necessary 2010-11-15 22:19:22 +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 Peek inside the StingText.properties to make sure the version in the properties matches the build version. 2011-02-03 18:07:55 +00:00
ivy.xml Working implementation of GATKRunReport POSTing to Amazon Web Services S3 storage. Requires users to explicitly provide the secret key to do the upload. Am investigating options to avoid having to do this in the future. Pretty cool little experiment for those who are interested in S3 interaction (extremely trivial) 2011-01-30 21:23:54 +00:00