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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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hanna d4ee999ef9 Creates files supplemental to the reference sequence, consumed by BWA. 
ANN - Alternate form of the sequence dictionary.  Should be created from a sequence dictionary with full contig names.
AMB - A map of 'holes' in the genome, aka runs of non-ACGTacgt bases.  This skeletal implementation always reports no
      holes.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2455 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-12-28 21:40:44 +00:00
R Sites that were marked NO_DINUC no longer get dinuc-corrected but are still recalibrated using the other available covariates. Solid cycle is now the same as Illumina cycle pending an analysis that looks at the effect of PrimerRoundCovariate. Solid color space methods cleaned up to reduce number of calls to read.getAttribute(). Polished NHashMap sort method in preparation for move to core/utils. Added additional plots in AnalyzeCovariates to look at reported quality as a function of the covariate. 2009-12-28 20:19:37 +00:00
archive Move VariantAnnotator over to use a StratifiedAlignmentContext split by sample. 2009-12-11 05:28:28 +00:00
c Add a Unix-standard version number to the file. 2009-11-23 20:07:17 +00:00
doc moved to wiki 2009-07-22 16:35:23 +00:00
java Creates files supplemental to the reference sequence, consumed by BWA. 2009-12-28 21:40:44 +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 Adding a package description for making a version of the GATK that only includes the FixBAMSortOrderTag walker. 2009-12-22 00:35:24 +00:00
perl /tmp is failing... 2009-10-08 18:13:49 +00:00
python Updated SNP calling power from coverage tools to work with new UnifiedGenotyper and DepthOfCoverage tools. 2009-12-16 20:44:30 +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 Update picard public and private to match new SAM update. 2009-12-23 22:34:12 +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 Clean up some of the walker help output based on additional experience and 2009-12-07 21:33:11 +00:00
ivy.xml New VariantFiltration. 2009-11-20 19:50:26 +00:00