gatk3的最后一个经典版本3.8

depristo c91712bd59 BAQ calculation refactoring in the GATK. Single -baq argument can be NONE, CALCULATE_AS_NECESSARY, and RECALCULATE. Walkers can control bia the @BAQMode annotation how the BAQ calculation is applied. Can either be as a tag, by overwriting the qualities scores, or by only returning the baq-capped qualities scores. Additionally, walkers can be set up to have the BAQ applied to the incoming reads (ON_INPUT, the default), to output reads (ON_OUTPUT), or HANDLED_BY_WALKER, which means that calling into the BAQ system is the responsibility of the individual walker. ... SAMFileWriterStub now supports BAQ writing as an internal feature. Several walkers have the @BAQMode applied to this, with parameters that I think are reasonable. Please look if you own these walkers, though git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4798 348d0f76-0448-11de-a6fe-93d51630548a		2010-12-06 20:55:52 +00:00
R	1)	2010-11-30 21:08:25 +00:00
archive	Fisher exact makes a return. Seems to be working properly. Current tagged as a work in progress. Needs to take the filtered context to be truly correct.	2010-10-22 20:35:53 +00:00
c	Reduce file handle usage.	2010-01-05 18:03:01 +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	BAQ calculation refactoring in the GATK. Single -baq argument can be NONE, CALCULATE_AS_NECESSARY, and RECALCULATE. Walkers can control bia the @BAQMode annotation how the BAQ calculation is applied. Can either be as a tag, by overwriting the qualities scores, or by only returning the baq-capped qualities scores. Additionally, walkers can be set up to have the BAQ applied to the incoming reads (ON_INPUT, the default), to output reads (ON_OUTPUT), or HANDLED_BY_WALKER, which means that calling into the BAQ system is the responsibility of the individual walker.	2010-12-06 20:55:52 +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	Updated the Queue GATK generator and packaging to include more dependencies for fullCallingPipeline.q.	2010-11-30 15:29:40 +00:00
perl	A helper script to merge two VCFs, run VariantEval, and the VariantReport.R script.	2010-11-28 00:45:21 +00:00
python	Trival changes to data processing paper python	2010-12-01 14:57:14 +00:00
ruby	accidentally commited an old tool	2010-08-25 15:42:02 +00:00
scala	With multi-sample genotyping must come scatter+gather. Also Khalid informed me of the .group(size) method, so removing my useless (but pretty) code.	2010-12-06 20:12:23 +00:00
settings	Added status email support with -statusTo. Will send emails on failure of an individual function or success/failure of the whole pipeline.	2010-10-14 15:58:52 +00:00
shell	Useful script for me	2010-11-18 15:21:06 +00:00
testdata	VQSR now operates on LOD scores in the INFO field directly, and doesn't adjust the QUAL field. New format for tranches file uses LOD score. Old file format no longer supported. log10sumlog10() function, a very useful utility in MathUtils. No more ExtendedPileupElement! Robust math calculations in GMM so that no infinities are generated! HaplotypeScore refactored to enable use of filtered context. Not yet enabled... InferredContext getDouble and getInteger arguments now parse values from Strings if necessary	2010-11-15 22:19:22 +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	Added the ability to test pipelines in dry or live mode via 'ant pipelinetest' and 'ant pipelinetest -Dpipeline.run=run'.	2010-11-22 22:59:42 +00:00
ivy.xml	Updated PluginManager so that during testing Queue can dynamically compile and load separately multiple class directories into the same class loader.	2010-11-12 20:14:28 +00:00