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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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depristo ec83a4b765 Initial commit, without any tool changes, of a new infrastructure for determining tranches. This new version walker up from the lowest quality snps and determines Ti/Tv. This is marginally more stable than moving in the other direction when there are few novel variants (exomes). Can make a substantial difference in the size of the call set (10-20%). I'll hook it into the main system now. Includes an new class Tranche, isolated read/writing utilities that are now testing in TestVariantRecalibrator, which should be moved to UnitTest as soon as I can figure out how to do this on my mac. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4654 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-11-11 23:52:49 +00:00
R now prints a nice report, can be invoked from command line 2010-11-09 19:44:10 +00:00
archive Fisher exact makes a return. Seems to be working properly. Current tagged as a work in progress. Needs to take the filtered context to be truly correct. 2010-10-22 20:35:53 +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 Initial commit, without any tool changes, of a new infrastructure for determining tranches. This new version walker up from the lowest quality snps and determines Ti/Tv. This is marginally more stable than moving in the other direction when there are few novel variants (exomes). Can make a substantial difference in the size of the call set (10-20%). I'll hook it into the main system now. Includes an new class Tranche, isolated read/writing utilities that are now testing in TestVariantRecalibrator, which should be moved to UnitTest as soon as I can figure out how to do this on my mac. 2010-11-11 23:52:49 +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 include the codecs into the RMD indexer that are available in the GATK, not just Tribble 2010-11-11 06:35:04 +00:00
perl Also removed contig intervals from the pipeline sanity check perl scsript. 2010-10-21 11:23:34 +00:00
python V1 of the data processing paper, produced results for the manuscript we presented. Commit for archival purposes 2010-11-11 01:43:21 +00:00
ruby accidentally commited an old tool 2010-08-25 15:42:02 +00:00
scala Moving all file cleanup to IOUtils for easier debugging. 2010-11-10 21:00:58 +00:00
settings Added status email support with -statusTo. Will send emails on failure of an individual function or success/failure of the whole pipeline. 2010-10-14 15:58:52 +00:00
shell Inprocess functions by default now log what output files they are running for. 2010-10-07 19:08:02 +00:00
testdata Fixes for example bam files 2010-10-05 18:43:02 +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 GSA-413 Explicitly set all compilers to use 512m memory maximum instead of 64m default maximum and running them out of the ant process. 2010-11-09 19:32:19 +00:00
ivy.xml Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00