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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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carneiro 4b9b767eb1 SelectVariants: now keeps the YAML stuff internal... it's there if you wanna use it, but won't be published anymore. Official parameter is the string for now. 
VariantEval: now sports the new MendelianViolation utility class.
MendelianViolationClassifier: I noticed I had broken chartl's walker by changing VariantEval, so I took the liberty to modify it to use the new library too, though I kept modifications to a minimum, could have gone into full integration if this is a useful tool, but since it's in oneoffs, I decided not to go all out.
MendelianViolation: Some getter methods were added for chartl and VariantEval.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5447 348d0f76-0448-11de-a6fe-93d51630548a
 		2011-03-15 18:36:55 +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 SelectVariants: now keeps the YAML stuff internal... it's there if you wanna use it, but won't be published anymore. Official parameter is the string for now. 2011-03-15 18:36:55 +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 Adding the native jna support libraries from the jna.jar to the Queue package jar. 2011-01-08 10:48:30 +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 One last little thing, I swear 2011-03-11 17:37:40 +00:00
ruby accidentally commited an old tool 2010-08-25 15:42:02 +00:00
scala Added an optional tag argument RodBind, similar to the Tag argument on TaggedFile. 2011-03-14 17:49:03 +00:00
settings Update Picard / sam-jdk at Tim's request. 2011-01-03 02:17:25 +00:00
shell While generating YAML now warning and skipping TSV rows that don't have all values. 2011-02-25 20:50:03 +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 Added another erroronmissingdir="false" for packging external dirs. 2011-03-14 21:26:28 +00:00
ivy.xml Added commons math, for Kristian. 2011-02-14 18:57:21 +00:00