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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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asivache d85461c463 MergingIterator completely re-done. Now it is not a generic class (sorry guys), but rather it is tailored for merging ROD tracks. This implementation peeks the locations of next ROD annotations in each track, but does not actually read these RODs from underlying streams until the location is reached and it is time to actually return the object. Now underlying ROD track iterators (registered in the resource pool!) are not advanced prematurely past the current position and all the way to the next ROD record wherever it is, so that the sharding system can reuse them. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2582 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-01-14 17:43:36 +00:00
R Update to AnalyzeCovariates to make the histogram of PairedReadOrder look a little nicer 2010-01-13 20:26:31 +00:00
archive Home for retired duplicateQuals analysis utility 2010-01-06 15:05:00 +00:00
c Reduce file handle usage. 2010-01-05 18:03:01 +00:00
doc moved to wiki 2009-07-22 16:35:23 +00:00
java MergingIterator completely re-done. Now it is not a generic class (sorry guys), but rather it is tailored for merging ROD tracks. This implementation peeks the locations of next ROD annotations in each track, but does not actually read these RODs from underlying streams until the location is reached and it is time to actually return the object. Now underlying ROD track iterators (registered in the resource pool!) are not advanced prematurely past the current position and all the way to the next ROD record wherever it is, so that the sharding system can reuse them. 2010-01-14 17:43:36 +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 b37 reference files and dbsnp 130 rods to resources 2010-01-14 03:28:22 +00:00
perl /tmp is failing... 2009-10-08 18:13:49 +00:00
python Minor changes (additional info calculated) 2010-01-06 16:41:01 +00:00
ruby Adding the ruby directory, and a simple script to restart Bamboo 2009-12-03 22:48:48 +00:00
scala/src Scala walkers can now be build and run like any other walker in the GATK. Added the getUrlsForClasspath to PackageUtils, the Reflections package isn't getting the manifest files from jars in the classpath, and so we weren't seeing any walkers outside of the GenomeAnalysisTK.jar. 2009-11-02 06:02:41 +00:00
settings New Picard and SAM-JDK with automatic sequence name truncation 2010-01-11 20:49:13 +00:00
shell Renaming error to getNegLog10PError(); added Cached clearing method to GL; SSG now has a CallResult that counts calls; No more Adding class to System.out, now to logger.info; First major testing piece (and general approach too) to unit testing of a walker -- SingleSampleGenotyper now knows how many calls to make on a particular 1mb region on NA12878 for each call type and counts the number of calls *AND* the compares the geli MD5 sum to the expected one! 2009-09-04 12:39:06 +00:00
testdata GSA-182: Adding support for BED interval files. 2009-10-06 02:45:31 +00:00
build.xml For Alec, and others at the Broad who want to run our unit/integration tests off of gsa1/gsa2: put a ceiling on the amount of memory that integration tests can use. Reduce the memory footprint of the fasta reader test. 2009-12-28 23:42:46 +00:00
ivy.xml New VariantFiltration. 2009-11-20 19:50:26 +00:00