gatk3的最后一个经典版本3.8

aaron b3bdcd0e60 make sure we close the error log stream in CommandLineProgram if it's opened; unit tests and clean-up for BasicVariation ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2241 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-03 06:59:27 +00:00
R	Added comments to AnalyzeCovariates and R scripts. R script prevents residuals from going off the edge of the plot. Added skeleton code to the recalibration walkers showing how we plan to handle SOLID reference inserting behavior.	2009-12-02 23:15:52 +00:00
archive	Initial checkin of AnalyzeCovariates.java which replaces analyzeRecalQuals_1KG.py and is updated to use the new Covariates system. It creates similar plots of residual error for each covariate that was used in the calculation. There is also an option to filter out base qualities below a given threshold.	2009-12-02 16:47:35 +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	make sure we close the error log stream in CommandLineProgram if it's opened; unit tests and clean-up for BasicVariation	2009-12-03 06:59:27 +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	Removed ReadQualityRecalibrator.xml	2009-12-02 20:14:14 +00:00
perl	/tmp is failing...	2009-10-08 18:13:49 +00:00
python	Minor updates to correctly handle emitting FN calls	2009-12-02 22:53:17 +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	Push version number of picard-private-parts	2009-11-25 19:28:57 +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	adding the option to not halt after a test failure; it will still report failure at the end. This makes sense for Bamboo so we know all the tests that fail, not just the first. It is also useful for checking what tests are affected by a change.	2009-12-03 06:19:39 +00:00
ivy.xml	New VariantFiltration.	2009-11-20 19:50:26 +00:00