gatk3的最后一个经典版本3.8

chartl 4c04c5a47a Addition of a BedTableCodec to allow for parsing of Bed-formatted tables (e.g. bedGraphs). Fixes for the recalibrator. Implementation of the data whitening input. Some TODOs in the RAW. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5529 348d0f76-0448-11de-a6fe-93d51630548a		2011-03-28 21:35:09 +00:00
R	Misc changes	2011-02-26 15:35:49 +00:00
analysis/depristo	Walkers can now specify a class extending from Gatherer to merge custom output formats. Add @Gather(MyGatherer.class) to the walker @Output.	2011-03-24 14:03:51 +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	Addition of a BedTableCodec to allow for parsing of Bed-formatted tables (e.g. bedGraphs). Fixes for the recalibrator. Implementation of the data whitening input. Some TODOs in the RAW.	2011-03-28 21:35:09 +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	Walkers can now specify a class extending from Gatherer to merge custom output formats. Add @Gather(MyGatherer.class) to the walker @Output.	2011-03-24 14:03:51 +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	A helper script that will take a list of bams, a list of case sample IDs, and a list of control sample IDs, and generate a sample meta data yaml (which includes the bamfiles)	2011-03-21 16:11:55 +00:00
ruby	accidentally commited an old tool	2010-08-25 15:42:02 +00:00
scala	Added BWA (option) to the data processing pipeline. Lots of testing still happening...	2011-03-28 20:17:57 +00:00
settings	Update Picard / sam-jdk at Tim's request.	2011-01-03 02:17:25 +00:00
shell	Fixing this so it gets the right 129 dbsnp for b37 samples	2011-03-22 17:43:20 +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	Build.xml contained references to tools now in picard	2011-03-17 18:29:46 +00:00
ivy.xml	Added commons math, for Kristian.	2011-02-14 18:57:21 +00:00