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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 0105e8d063 Updated Queue GATK generation to reflect -B and -I changes. 
To add support for "-I:tumor tumor.bam", the GATK argument
import_file (-I) is now generated as a List of NamedFile objects.
Could not get sugar working 100%.  To activate sugar import the
gatk package.  This effectively adds a new method to java.io.File
called toNamedFile.  When adding a file to the list call
  countReads.import_file :+= myJavaFile.toNamedFile
See scala/qscript/examples for actual examples.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4122 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-08-25 22:17:36 +00:00
R Placeholder commit. Implements a loader for a new multi-part GATK reporting format. See what it looks like at /home/radon01/kiran/scr1/projects/NewVariantEvalOutput/results/v1/tableexample.txt . Still need to address the issue where numeric columns are being interpreted as a vector of strings, not numbers. 2010-08-25 18:48:44 +00:00
archive Archiving 2010-07-27 02:47:18 +00:00
c Reduce file handle usage. 2010-01-05 18:03:01 +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 Updated Queue GATK generation to reflect -B and -I changes. 2010-08-25 22:17:36 +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 Enabling support for any scala used in QScripts. 2010-08-17 22:05:56 +00:00
perl update to use new rod syntax 2010-08-25 20:21:53 +00:00
python updated to deal with new cleaning pipeline outputs and potentially infinity TI/TV 2010-08-24 16:01:09 +00:00
ruby accidentally commited an old tool 2010-08-25 15:42:02 +00:00
scala Updated Queue GATK generation to reflect -B and -I changes. 2010-08-25 22:17:36 +00:00
settings 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
shell Useful script to see the status of gsa computing resources. Crontab'd and will be arriving as email at 8 am 2010-08-07 12:36:28 +00:00
testdata and add changes to the vcf used in testing 2010-06-25 02:56:02 +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 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
ivy.xml Okay, finally done with VCF compression. Now: 2010-08-24 16:36:54 +00:00