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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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chartl 88a06ad81f Changes to Depth of Coverage: 
- For speedup in large number of samples, base counts are done on a per read group level, then
   merged into counts on larger partitions (samples, libraries, etc)
   + passed all integration tests before next item
- Added additional summary item, a coverage threshold. Set by (possibly multiple) -ct flags,
   the summary outputs will have columns for "%_bases_covered_to_X"; both per sample, and
   per sample per interval summary files are effected (thus md5s changed for these)

NOTE:

This is the last revision that will include the per-gene summary files. Once DesignFileGenerator is sufficiently general, and has integration tests, it will be moved to core and the per-gene summary from Depth of Coverage will be retired.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3437 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-05-26 03:39:22 +00:00
R Variant Optimizer accepts a dbSNP rod arugment to use in determining known/novel status as opposed to using the rsID in the vcf record. VO generates plots of annotation values used in clustering broken out by knowns and novels. Useful for showing which annotations are approximately Gaussian. 2010-05-09 16:48:07 +00:00
archive Retiring multi-sample genotyper 2010-05-20 14:11:11 +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 Changes to Depth of Coverage: 2010-05-26 03:39:22 +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 without the *, the package system only took directly referenced files (which pulled in VCF and BED) but skipped dbsnp. Epic star fail... 2010-05-24 05:19:57 +00:00
perl Add argument to sortByRef for specifying the tmp directory for sorting. 2010-05-07 13:53:26 +00:00
python minor change for eric 2010-05-21 20:13:36 +00:00
ruby Adding the ruby directory, and a simple script to restart Bamboo 2009-12-03 22:48:48 +00:00
scala/src Refactoring and sugar to give lower level access to the job graph. 2010-05-25 22:52:29 +00:00
settings revisioning tribble to version 85, which includes tabix and bug fixes 2010-05-25 04:28:32 +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 a small dbsnp file for Tribble testing 2010-02-18 18:12:55 +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 A cleaned up functioning early, early access version of Queue for others to play with and provide feedback about next steps. 2010-05-23 20:21:09 +00:00
ivy.xml A cleaned up functioning early, early access version of Queue for others to play with and provide feedback about next steps. 2010-05-23 20:21:09 +00:00