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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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ebanks c6ad26e04f 1) When quals/GQs are really integers (x.00), strip off the floating points. 
2) Keep track of whether vcf records are unfiltered vs. pass filters in the variant context so we can regenerate the records on output.
3) No more "ID" hard-coded all over the code to set the VariantContext ID.  Use a static variable instead.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3840 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-07-20 18:01:45 +00:00
R A very nice way of automatically plotting the results of a VariantEval run. All of the hard work is actually in the common R repository, gsacommons.R, including methods for creating a Venn diagram. It also provides a mechanism for the output of a VariantEval run to be loaded into a single list object. 2010-07-19 12:38:26 +00:00
archive 1. Refactoring of GenoypeWriters so that parallelization now works again with VCF4.0. We now have just a single reference to the old VCF classes, and that one will be purged soon. 2010-07-20 06:16:45 +00:00
c Reduce file handle usage. 2010-01-05 18:03:01 +00:00
doc moved to wiki 2009-07-22 16:35:23 +00:00
java 1) When quals/GQs are really integers (x.00), strip off the floating points. 2010-07-20 18:01:45 +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 Add CountFunctionalVariants to local release (for firehose) 2010-07-17 01:36:16 +00:00
perl 1. Updated tests and added integration test for liftover code. 2010-07-12 17:58:18 +00:00
python Improvements to 1KG processing pipeline 2010-07-16 15:33:47 +00:00
ruby Adding the ruby directory, and a simple script to restart Bamboo 2009-12-03 22:48:48 +00:00
scala 1KG Table 1 counting pipeline. Useful example 2010-07-17 22:30:56 +00:00
settings updating the Tribble library; added writing of indexes to the index interface for working with the tree index. 2010-07-20 07:02:08 +00:00
shell a) Add input argument (-ncrate) to BeagleOutputToVCFWalker. If the genotype posterior error probability is higher than this threshold, we declare No-call at this genotype. 2010-07-06 18:33:28 +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 adding Ivy lines for findbug, and adding a build task (to run it locally you need to have installation of findbug). I'll put more information on the wiki when it's up and running. 2010-07-08 19:10:19 +00:00
ivy.xml adding the annotations for findbugs as dependencies in the GATK. They have to be in the default config so that we can 2010-07-19 16:34:57 +00:00