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gatk3的最后一个经典版本3.8
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chartl 341e93ee12 The reference fixer seems to have munged the OMNI rather than making it better. Looks like some sites need to only have the ref and alt bases swapped, and others need to have the genotypes swapped as well? E.g. 
some subset need
A  C  1/1   -->  C  A  0/0

while another subset need
A  C  1/1   -->  C  A  1/1

it's unclear how big these subsets are (or even if one is empty). What I do know is, doing the first one totally screws up concordance metrics for the 421-sample chip. So either something else needs to be done, or there's a bug in this walker. Until I know for sure, I've added an initialize exception to disable this thing...



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4523 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-10-19 12:50:24 +00:00
R Better reporting -- figured out how to drop unused levels in subset 2010-10-06 14:31:51 +00:00
archive Cleaning up playground utils and tests 2010-08-27 01:25:47 +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 The reference fixer seems to have munged the OMNI rather than making it better. Looks like some sites need to only have the ref and alt bases swapped, and others need to have the genotypes swapped as well? E.g. 2010-10-19 12:50:24 +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 Include all standard annotations 2010-10-11 20:52:08 +00:00
perl Using James P's patch for the liftover script 2010-10-18 01:44:54 +00:00
python Adding a script to do big table conversion. Removing Ben's script which is totally obsolete and busted. 2010-10-12 01:40:43 +00:00
ruby accidentally commited an old tool 2010-08-25 15:42:02 +00:00
scala QScript authors can now tag functions as intermediate. Functions tagged as intermediate will be skipped unless another function in the graph needs their output. 2010-10-18 22:11:14 +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 Inprocess functions by default now log what output files they are running for. 2010-10-07 19:08:02 +00:00
testdata Fixes for example bam files 2010-10-05 18:43:02 +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 Wrapping ScatterGatherableFunctions with a facade instead of using slower clone library. Will require keeping Clone's facade code in sync with CommandLineFunction but runs *much* faster. 2010-10-07 01:19:18 +00:00
ivy.xml 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