gatk3的最后一个经典版本3.8
 
 
 
 
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chartl 328f89f66a Minor changes to MannWhitneyU:
- Comment fixes to better explain why two-sided test wants to use the LOWER (not higher) value for U
 - Much more direct testing of MWU functions
 - Uniform approximation was always using the < cumulant (sometimes the > cumulant should be used instead)
 - Uniform approximation currently not used (regime in which it was being used was not the right one -- not necessarily bad, but not an improvement over normal)
    + this particular approximation is for major imbalances of the form m >> n. Code may be altered in the future to use this method for this particular regime, if the method's not too slow.
 - Hook into one-sided test.

RegionalAssociationRecalibrator: NaNs were being caused by presence of Infinity and -Infinity values out of the walker. Currently I'm just re-setting them to arbitrary post-whitened values, but the walker will be changed to prevent output of these values, and the "fix" will undone.




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5539 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-30 17:03:02 +00:00
R Misc changes 2011-02-26 15:35:49 +00:00
analysis/depristo Walkers can now specify a class extending from Gatherer to merge custom output formats. Add @Gather(MyGatherer.class) to the walker @Output. 2011-03-24 14:03:51 +00:00
archive Moving GLF code to archive 2011-01-15 22:42:42 +00:00
c Bug fixes for the bwa aligner and changes to support compiling against newer releases of the bwa code base. 2010-12-17 14:49:15 +00:00
doc removing the custom reflections library from the libs, and adding a release version. Hopefully this will fix the problem Menachem has been seeing with random JVM crashes. Also 2010-08-19 00:42:37 +00:00
java Minor changes to MannWhitneyU: 2011-03-30 17:03:02 +00:00
lua forgot to remove a debug line. 2011-02-15 16:25:48 +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 Walkers can now specify a class extending from Gatherer to merge custom output formats. Add @Gather(MyGatherer.class) to the walker @Output. 2011-03-24 14:03:51 +00:00
perl 2 more scripts I found helpful in syncing (and cleaning up) the 1000G mirror 2011-02-22 04:17:36 +00:00
python A helper script that will take a list of bams, a list of case sample IDs, and a list of control sample IDs, and generate a sample meta data yaml (which includes the bamfiles) 2011-03-21 16:11:55 +00:00
ruby accidentally commited an old tool 2010-08-25 15:42:02 +00:00
scala Count Covariates is almost scatter-gatherable now! 2011-03-29 22:25:33 +00:00
settings Update Picard / sam-jdk at Tim's request. 2011-01-03 02:17:25 +00:00
shell Fixing this so it gets the right 129 dbsnp for b37 samples 2011-03-22 17:43:20 +00:00
testdata ReplaceReadGroups. Fixes BAM files without read group info. MissingReadGroup points people to this tool now. Please point users on the forum to this tool now. Will migrate to Picard. 2011-02-21 14:02:41 +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 Build.xml contained references to tools now in picard 2011-03-17 18:29:46 +00:00
ivy.xml Added commons math, for Kristian. 2011-02-14 18:57:21 +00:00