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gatk3的最后一个经典版本3.8
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257 MiB
Java 95.8%
Scala 3.8%
R 0.2%
JavaScript 0.1%
 
 
 
 
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chartl 8740124cda @ListUtils - Bugfix in getQScoreOrderStatistic: method would attempt to access an empty list fed into it. Now it checks for null pointers and returns 0. 
@MathUtils - added a new method: cumBinomialProbLog which calculates a cumulant from any start point to any end point using the BinomProbabilityLog calculation.

@PoolUtils - added a new utility class specifically for items related to pooled sequencing. A major part of the power calculation is now to calculate powers
             independently by read direction. The only method in this class (currently) takes your reads and offsets, and splits them into two groups
             by read direction.

@CoverageAndPowerWalker - completely rewritten to split coverage, median qualities, and power by read direction. Makes use of cumBinomialProbLog rather than
                          doing that calculation within the object itself.




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1462 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-08-27 19:31:53 +00:00
R Updated python files 2009-07-07 14:15:39 +00:00
c Move non-java code out of playground. 2009-03-23 19:31:38 +00:00
doc moved to wiki 2009-07-22 16:35:23 +00:00
java @ListUtils - Bugfix in getQScoreOrderStatistic: method would attempt to access an empty list fed into it. Now it checks for null pointers and returns 0. 2009-08-27 19:31:53 +00:00
packages adding the package description for the VCF validator 2009-08-20 04:46:27 +00:00
perl Now you can specify '-' instead of input file name, and the script will read from stdin 2009-08-14 20:30:56 +00:00
python Added command line options to make the barcode analysis script executable by end users. 2009-08-24 21:15:09 +00:00
settings Switched to Reflections (http://code.google.com/p/reflections/) project for 2009-07-21 18:32:22 +00:00
shell Version 0.2.1 (released) of the TableRecalibrator 2009-06-25 22:50:55 +00:00
testdata 2009_02 release is no longer with us. Update the bam list. 2009-08-11 12:49:23 +00:00
build.xml Exclude secondary base caller code from playground jar. Still TODO: figure 2009-07-30 21:02:46 +00:00
ivy.xml Switched to Reflections (http://code.google.com/p/reflections/) project for 2009-07-21 18:32:22 +00:00