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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 bc17ff567a When you get the reference string for a read that is mapped partially off the end of a contig, the string is masked with X's for base positions without corresponding reference positions. Now with a test case! 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1156 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-07-02 14:15:50 +00:00
R Version 0.2.1 (released) of the TableRecalibrator 2009-06-25 22:50:55 +00:00
c Move non-java code out of playground. 2009-03-23 19:31:38 +00:00
doc up on the wiki, removing it from the repo. Ignore my last commit 2009-07-01 15:42:02 +00:00
java When you get the reference string for a read that is mapped partially off the end of a contig, the string is masked with X's for base positions without corresponding reference positions. Now with a test case! 2009-07-02 14:15:50 +00:00
packages added the example files to the distro 2009-07-01 23:16:42 +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 Version 0.2.1 (released) of the TableRecalibrator 2009-06-25 22:50:55 +00:00
settings Updates to picard public / private and sam. 2009-06-30 14:50:55 +00:00
shell Version 0.2.1 (released) of the TableRecalibrator 2009-06-25 22:50:55 +00:00
testdata bam and fasta files generated with the artificial tools. These will be included in the GATK distro. 2009-07-01 22:49:31 +00:00
build.xml Convert the somatic coverage tool to output from the packaging tool rather than from the dist target. 2009-06-18 21:29:30 +00:00
ivy.xml Add bcel and cleanup. 2009-06-17 19:28:04 +00:00