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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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droazen 44a29680bf Explicitly marked the updated tribble jar added in r5982 as binary 
(Oh yes, there was a r5982, in case you were wondering. It was the first
tentative git -> svn commit, and just added an updated tribble jar. It went great except for the fact that svn didn't mark the jar as binary, causing a textual diff for 500k of binary data to be generated in the notification email, cause Gsa_svn_list to very probably choke on the notification email rather than deliver it. Now let us never speak of r5982 again...) 


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5983 348d0f76-0448-11de-a6fe-93d51630548a
 		2011-06-13 18:37:48 +00:00
R Oops, forgot one tiny thing 2011-06-13 17:12:42 +00:00
analysis/depristo CalibrateGenotypeLikelihoods now emits a molten data set with REF and ALT alleles, so that GL calibration can be evaluated as a function of the REF/ALT bases. DigestTable is a stand-alone Rscript that digests the multi-GB molten data table into a tiny table that shows reported vs. empirical GLs, as a function of a variety of features of the data, like REF/ALT, comp GT, eval GT, and GL itself. 2011-05-21 14:02:30 +00:00
archive Removed unused importants, but some of these scripts are now out of date (they have been for a long time) so they don't compile anyway 2011-05-22 18:43:48 +00:00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
chainFiles Renamed for consistency 2011-05-25 02:12:21 +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 Better error message for the case of input variants found in ApplyRecalibration that were never seen during VariantRecalibrator. 2011-06-13 14:45:28 +00:00
lua cleaned up the scripts and created an interval library to facilitate future reuse. 2011-05-27 19:35:36 +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 Added cofoja to the Queue package. Although BCEL doesn't think they're needed the scala compiler respectfully disagrees. 2011-05-26 17:42:34 +00:00
perl Quit immediately with an error message if any of the individual steps fails. 2011-04-22 13:23:33 +00:00
python (Hopefully) short-lived script to rework the directory structure from core / 2011-06-08 19:18:22 +00:00
ruby accidentally commited an old tool 2010-08-25 15:42:02 +00:00
scala V1 of the post processing QC plotting scala script and R function. The scala script runs VariantEval on a VCF file, and computes QC metrics. The R script generates the report. Will discuss usage with data processing group. Ryan -- please add your additional plotting routines to this script, as you see fit. 2011-06-13 17:06:42 +00:00
settings Updated the tribble jar 2011-06-13 18:00:09 +00:00
shell Useful utility for looking at the file size of GSA file systems 2011-04-02 03:47:27 +00:00
testdata Updating VariantGaussianMixtureModelUnitTest to use truth sensitivity cutting 2011-05-04 13:56:01 +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 Fix for CoFoJa exception by upgrading to latest version 2011-06-09 17:49:15 +00:00
ivy.xml Factor out all testing dependencies into a separate test configuration and 2011-05-05 22:42:11 +00:00