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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 751aa8bfa6 Partial rewrite of the summary metrics aggregator to accumulate all metrics 
from sample-level summaries, rather than only specific metrics.  Continues to
manually handle fingerprinting.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6038 348d0f76-0448-11de-a6fe-93d51630548a
 		2011-06-22 22:53:53 +00:00
R Removed nDeletions and nInsertions as independent plots -- just not useful given nIndels and insertions/deletion ratio. Fixed jitter problems with rug plots by removing the rugs entirely. Recovered, and improved, comparative features lost by removing the rug plots by getting viewports to work (trivial) so now per sample metrics and distributions are displayed on the same page! 2011-06-22 13:59:46 +00:00
analysis/depristo Simple program that calls indels in CEU trio exomes and WGS can compared the results. Overall the indel calls really look good to me, given reasonably good input BAM files. 2011-06-16 12:56:04 +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archive Removed unused importants, but some of these scripts are now out of date (they have been for a long time) so they don't compile anyway 2011-05-22 18:43:48 +00:00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 bye bye 2011-06-22 22:53:42 +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 Oops. Failed to add DbSnpMatchMetrics to Picard private jar. 2011-06-14 15:14:19 +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 Partial rewrite of the summary metrics aggregator to accumulate all metrics 2011-06-22 22:53:53 +00:00
ruby accidentally commited an old tool 2010-08-25 15:42:02 +00:00
scala Putting new association files, some qscripts, and the new pick sequenom probes file under local version control. I notice some dumb emacs backup files, I'll kill those off momentarily. Also minor changes to GenomeLoc (getStartLoc() and getEndLoc() convenience methods) 2011-06-22 22:53:37 +00:00
settings Updated the tribble jar to revision 345 2011-06-22 22:53:25 +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 A prototype script and library dependencies to extract a BAM list from a 2011-06-22 22:53:45 +00:00