gatk3的最后一个经典版本3.8

droazen 658e65d26c 2 unrelated changes: 1) fix the variant context adaptor for dbsnp; conversion of deletions was totally broken. 2) stop using paths that include gsa-scr1 in integration tests. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6070 348d0f76-0448-11de-a6fe-93d51630548a		2011-06-22 22:56:07 +00:00
R	Checkpointing some bugfixes with zero-length version directories and missing	2011-06-22 22:56:01 +00:00
analysis/depristo	Simple program that calls indels in CEU trio exomes and WGS can compared the results. Overall the indel calls really look good to me, given reasonably good input BAM files.	2011-06-16 12:56:04 +00:00
archive	Binomial and Multinomial interfaces for probability and coefficients in log and real space. Passed all unit tests.	2011-06-22 22:55:15 +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
chainFiles	Renamed for consistency	2011-05-25 02:12:21 +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	2 unrelated changes: 1) fix the variant context adaptor for dbsnp; conversion of deletions was totally broken. 2) stop using paths that include gsa-scr1 in integration tests.	2011-06-22 22:56:07 +00:00
lua	added comments on how to use this very useful script!	2011-06-22 22:55:50 +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	Oops. Failed to add DbSnpMatchMetrics to Picard private jar.	2011-06-14 15:14:19 +00:00
perl	Quit immediately with an error message if any of the individual steps fails.	2011-04-22 13:23:33 +00:00
python	Checkpointing some bugfixes with zero-length version directories and missing	2011-06-22 22:56:01 +00:00
ruby	accidentally commited an old tool	2010-08-25 15:42:02 +00:00
scala	now with the new 'consensus model' parameter to the cleaner.	2011-06-22 22:55:42 +00:00
settings	Updated the tribble jar to revision 351	2011-06-22 22:55:57 +00:00
shell	Useful utility for looking at the file size of GSA file systems	2011-04-02 03:47:27 +00:00
testdata	Updating VariantGaussianMixtureModelUnitTest to use truth sensitivity cutting	2011-05-04 13:56:01 +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	Fix for CoFoJa exception by upgrading to latest version	2011-06-09 17:49:15 +00:00
ivy.xml	A prototype script and library dependencies to extract a BAM list from a	2011-06-22 22:53:45 +00:00