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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 a32245f7d2 Modifications: 
QualityUtils - Stole the BaseUtils code for flipping reads around and applied it to quality scores
SecondBaseSkew - Nothing's really different, just a commented line

Additions (experimental annotations for future development of second-base annotation)
** I DO NOT INTEND FOR ANYONE TO USE THESE **
- ProportionOfNonrefBasesSupportingSNP
- ProportionOfSNPSecondBasesSupportingRef
- ProportionOfRefSecondBasesSupportingSNP
  + I hope these are self-explanatory
- QualityAdjustedSecondBaseLod
  + Adjust lod-score by 10*log10[P[second bases are as observed]]

Added walker:

QualityScoreByStrand - oneoff project that's being saved if i ever need it



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2527 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-01-06 19:18:07 +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 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 Modifications: 2010-01-06 19:18:07 +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 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 versions of picard-private, sam and picard jars for TileCovariate and regeneration of NM tag 2009-12-28 22:18:55 +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