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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 37fbf17da8 Finally restored code after accidentally removing three days worth of work: 
schedule file infrastructure has been restored, and is now a single file.
Only the exact bins required for the traversal are stored in the schedule.
Very close to being able to merge schedule entries.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5497 348d0f76-0448-11de-a6fe-93d51630548a
 		2011-03-23 05:52:40 +00:00
R Misc changes 2011-02-26 15:35:49 +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 Finally restored code after accidentally removing three days worth of work: 2011-03-23 05:52:40 +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 Using an embedded version of Picard for merging un-indexed bam files after scatter/gather instead of requiring the QScripts to specify the picard JAR. May do this for the GATK jar too. 2011-03-21 18:20:01 +00:00
perl 2 more scripts I found helpful in syncing (and cleaning up) the 1000G mirror 2011-02-22 04:17:36 +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 documentation changes to agree with the wiki 2011-03-22 21:48:49 +00:00
settings Update Picard / sam-jdk at Tim's request. 2011-01-03 02:17:25 +00:00
shell Fixing this so it gets the right 129 dbsnp for b37 samples 2011-03-22 17:43:20 +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 Build.xml contained references to tools now in picard 2011-03-17 18:29:46 +00:00
ivy.xml Added commons math, for Kristian. 2011-02-14 18:57:21 +00:00