gatk3的最后一个经典版本3.8

delangel 8c262eb605 Initial commit of new likelihood model to evaluate indel quality. Principle is simple, a plain Pair HMM with affine gap penalties (in log space) that does quasi-local alignment between reads and candidate haplotypes and which in theory should be more solid and more reliable than the older Dindel-based model. It also allows to be easily extensible in the future if we decide to introduce either context-dependent and/or read-dependent gap penalties. ... Model is disabled by default and we're still using the old Dindel model until I'm more confident that new model is a definitive improvement, so right now this is enabled by hidden command line arguments, and it's not to be used yet. In detail: a) Several refactorings to share softMax() available to other modules, so its now part of MathUtils. b) Refactored a couple of read utilities and moved from BAQ to ReadUtils. c) New PairHMMIndelErrorModel class implementing new likelihood model d) Several new hidden debug arguments in UAC. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5389 348d0f76-0448-11de-a6fe-93d51630548a		2011-03-07 15:31:58 +00:00
R	Misc changes	2011-02-26 15:35:49 +00:00
analysis/depristo	Scripts to create the GATK IAM user and give him/her rights to PutObject (and only PutObject) into the S3 storage instance. Updated the GATKRunReport to now upload using the GATK user, not mark@depristo.com. Running with -et AWS_S3 sends run reports up to the Amazon S3 cloud now. Going to request a few external users try this option so we can see it running at scale. I'm sure S3 can handle a few hundred thousand 1Kb uploads per days, though	2011-01-31 03:48:33 +00:00
archive	Moving GLF code to archive	2011-01-15 22:42:42 +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
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	Initial commit of new likelihood model to evaluate indel quality. Principle is simple, a plain Pair HMM with affine gap penalties (in log space) that does quasi-local alignment between reads and candidate haplotypes and which in theory should be more solid and more reliable than the older Dindel-based model. It also allows to be easily extensible in the future if we decide to introduce either context-dependent and/or read-dependent gap penalties.	2011-03-07 15:31:58 +00:00
lua	forgot to remove a debug line.	2011-02-15 16:25:48 +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	Adding the native jna support libraries from the jna.jar to the Queue package jar.	2011-01-08 10:48:30 +00:00
perl	2 more scripts I found helpful in syncing (and cleaning up) the 1000G mirror	2011-02-22 04:17:36 +00:00
python	Minor utility improvements	2011-02-26 15:36:26 +00:00
ruby	accidentally commited an old tool	2010-08-25 15:42:02 +00:00
scala	Finally figured out what data in the LSF C API call lsb_readjobinfo is causing JNA to SIGSEGV with a strlen error:	2011-03-07 04:29:06 +00:00
settings	Update Picard / sam-jdk at Tim's request.	2011-01-03 02:17:25 +00:00
shell	While generating YAML now warning and skipping TSV rows that don't have all values.	2011-02-25 20:50:03 +00:00
testdata	ReplaceReadGroups. Fixes BAM files without read group info. MissingReadGroup points people to this tool now. Please point users on the forum to this tool now. Will migrate to Picard.	2011-02-21 14:02:41 +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	fixed problem with Matt re: packaging commands from external walker codebases	2011-02-24 21:11:38 +00:00
ivy.xml	Added commons math, for Kristian.	2011-02-14 18:57:21 +00:00