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gatk3的最后一个经典版本3.8
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257 MiB
Java 95.8%
Scala 3.8%
R 0.2%
JavaScript 0.1%
 
 
 
 
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hanna 24ec35deaf - Reintroduce test dependency so that the tests passing / failing is not 
dependent on the contents of the integrationtest directory.  Will figure
  out how to better manage the integrationtest directory at some point in
  the future.
- Up the max heap size for tests.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4691 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-11-16 19:55:20 +00:00
R New version of cutting routines for VQSR. Old code removed. Working unit tests. Best practice with testng integration test (everyone look at it). Walker test now allows you to not specify no. input files, if it can infer input counts from MD5s 2010-11-13 16:19:56 +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 - Reintroduce test dependency so that the tests passing / failing is not 2010-11-16 19:55:20 +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 Script based on the second part of Eric's createTranscriptToGenomicInfoTables.pl script which sorts flat files by reference order 2010-11-15 19:44:32 +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 Fixing a silly typo 2010-11-15 18:16:51 +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 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 - Reintroduce test dependency so that the tests passing / failing is not 2010-11-16 19:55:20 +00:00
ivy.xml Updated PluginManager so that during testing Queue can dynamically compile and load separately multiple class directories into the same class loader. 2010-11-12 20:14:28 +00:00