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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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ebanks 8e149cc52f Fixing a silly bug of mine: when a realignment target begins at position 1 of a contig, it was possible to have some reads get emitted out of order (triggering an exception in the SAMFileWriter). This is fixed by moving around some parentheses. Tim, if you are reading this: feel free to take this fix in whenever it's convenient. I.e. it's not critical as the only user who has been hit by it has a reference with over 130K short contigs. Committing in SVN so that it gets incorporated immediately (and I can respond on GS now). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6024 348d0f76-0448-11de-a6fe-93d51630548a
 		2011-06-21 21:42:38 +00:00
R Now produces an expanded table at the start, as well 2011-06-20 13:45:08 +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archive Removed unused importants, but some of these scripts are now out of date (they have been for a long time) so they don't compile anyway 2011-05-22 18:43:48 +00:00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 Fixing a silly bug of mine: when a realignment target begins at position 1 of a contig, it was possible to have some reads get emitted out of order (triggering an exception in the SAMFileWriter). This is fixed by moving around some parentheses. Tim, if you are reading this: feel free to take this fix in whenever it's convenient. I.e. it's not critical as the only user who has been hit by it has a reference with over 130K short contigs. Committing in SVN so that it gets incorporated immediately (and I can respond on GS now). 2011-06-21 21:42:38 +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 Rev Picard to get new PF_INDEL_RATE metric. Rev preQC generator script 2011-06-14 17:43:43 +00:00
ruby accidentally commited an old tool 2010-08-25 15:42:02 +00:00
scala Added stratification by discrete allele count, just like AF, but requiring genotypes so it can be exact. Added docs on wiki, and integrationtest using Kiran's very nice fundamental VCF 2011-06-19 03:11:00 +00:00
settings Rev Picard to get new PF_INDEL_RATE metric. Rev preQC generator script 2011-06-14 17:43:43 +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