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gatk3的最后一个经典版本3.8
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chartl 7c9ef59d65 This is simultaneously a minor and major change to VariantEval, so take heed: 
The core walker has been modified so that when variant contexts (eval and comp) are subset to command-line-specified sample(s), the chromosome count annotations (AC/AN/AF) are altered to reflect the AC/AN/AF of only those samples involved in the comparison. No more getting AC500 when you're comparing a 10-sample overlap. Interestingly enough, this didn't break any integration tests.

GenotypeConcordance now has two additional tables: Allele Count Statistics, and Allele Count Summary Statistics. These work exactly identically to the Sample Statistics and Sample Summary Statistics tables, except that the partition being used is no longer the sample, but instead the allele count of the variant sites. These tables stratify by both eval and comp ACs, e.g.

evalAC0
evalAC1
evalAC2
compAC0
compAC1
compAC2

Differences with previous integration tests were verified to only be in the Allele Count tables (by grepping them out of the diff); a new test has been added for the simple case of an AC=1 site in the eval becoming an AC=2 site in the comp.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4491 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-10-13 22:26:15 +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 This is simultaneously a minor and major change to VariantEval, so take heed: 2010-10-13 22:26:15 +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 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
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 Emergency fix for Ryan: 2010-10-13 22:22:01 +00:00
settings 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
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 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