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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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aaron 107b5d73b5 The flagStatReadWalker generates the exact same statistical output as the samtools flagstat command, so the two outputs can be diff'ed. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@883 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-06-02 21:23:56 +00:00
c Move non-java code out of playground. 2009-03-23 19:31:38 +00:00
doc Added documentation for calling the GATK from Matlab. This is to document the extreme basic and experimental support for using Matlab to call the GATK, and is more of a placeholder for when we have time to revisit supporting this. 2009-05-13 15:25:51 +00:00
java The flagStatReadWalker generates the exact same statistical output as the samtools flagstat command, so the two outputs can be diff'ed. 2009-06-02 21:23:56 +00:00
perl checking in new folder for perl scripts AND a simple script that takes an input text file and reference dictionary (.fai) and performs stable sort of the input lines according to the contig order specified by the dictionary. Position of the contig filed to sort on in the input lines is specified as --k POS option. Input lines may specify contigs that are not in the dictionary, in this case the additional contigs will be added at the end of the sorted output, after all known contigs. The sorting order between these additional contigs is simply the order in which they first appear in the input 2009-05-27 16:34:55 +00:00
python more and better python scripts for dealing with calls 2009-06-02 20:37:19 +00:00
settings Update to latest version of picard. Change imports in all classes dependent on picard public from import edu.mit.broad.picard... to import net.sf.picard... 2009-05-28 20:13:01 +00:00
shell Adding a script for diff'ing the output of samtools and the GATK for the whole genome and each individual chromosome. 2009-06-02 21:19:39 +00:00
testdata Better interface to the tabular ROD, now makes writing files easier. Also has corresponding test files 2009-05-14 23:20:11 +00:00
build.xml We now only build the files that have changed. It should speed up compile time as our source tree grows. 2009-05-15 20:48:01 +00:00
ivy.xml Update to latest version of picard. Change imports in all classes dependent on picard public from import edu.mit.broad.picard... to import net.sf.picard... 2009-05-28 20:13:01 +00:00