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gatk3的最后一个经典版本3.8
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Scala 3.8%
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fromer 01c2091cd9 A LocusWalker to print the haploid reference genome as a VCF file 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4968 348d0f76-0448-11de-a6fe-93d51630548a
 		2011-01-10 16:59:41 +00:00
R Private mutation simulator and analysis routines for EOMI paper 2011-01-07 21:23:29 +00:00
archive Eric broke the build. Eric broke the build. 2010-12-15 17:01:38 +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 A LocusWalker to print the haploid reference genome as a VCF file 2011-01-10 16:59:41 +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 Deleting old python code 2011-01-07 21:33:45 +00:00
ruby accidentally commited an old tool 2010-08-25 15:42:02 +00:00
scala Removed stochasticity from IndelRealigner by random sampling using and seed based on the read list. 2011-01-07 22:03:36 +00:00
settings Update Picard / sam-jdk at Tim's request. 2011-01-03 02:17:25 +00:00
shell watch -n 30 shell/pipelineJobs.csh for those who want to watch the gsaadm's jobs progress 2011-01-09 13:09:30 +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 Removed stochasticity from IndelRealigner by random sampling using and seed based on the read list. 2011-01-07 22:03:36 +00:00
ivy.xml Removed stochasticity from IndelRealigner by random sampling using and seed based on the read list. 2011-01-07 22:03:36 +00:00