gatk3的最后一个经典版本3.8

hanna deab9f0aa5 Initial work on proto-shard merger: ... - create size() method that returns an approximation of the uncompressed size in bytes of BAM span. I'll use this method as a protoshard weighting function until we determine how to normalize the weights across the different data access mechanisms (reads, reference, RODs). - Implementations of basic union/intersection/subtraction mechanisms for BAM spans; should be enough to get an accurate weight for two proto-shards put together. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5541 348d0f76-0448-11de-a6fe-93d51630548a		2011-03-30 22:03:43 +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	Initial work on proto-shard merger:	2011-03-30 22:03:43 +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	When @Gather annotation is missing (probably due to an unclean build) printing out the full field+class name for debugging purposes.	2011-03-30 21:43:37 +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	When @Gather annotation is missing (probably due to an unclean build) printing out the full field+class name for debugging purposes.	2011-03-30 21:43:37 +00:00
ivy.xml	Added commons math, for Kristian.	2011-02-14 18:57:21 +00:00