gatk-3.8

gatk3的最后一个经典版本3.8

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ebanks a205900eff Naughty use of Strings in HaplotypeScore literally double the runtime of Unified Genotyper. Moved over to bytes and no longer allow Strings in the Haplotype util class. New round of profiling on tap for tomorrow. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4528 348d0f76-0448-11de-a6fe-93d51630548a		2010-10-20 03:32:21 +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	Naughty use of Strings in HaplotypeScore literally double the runtime of Unified Genotyper. Moved over to bytes and no longer allow Strings in the Haplotype util class. New round of profiling on tap for tomorrow.	2010-10-20 03:32:21 +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	Patch for James	2010-10-20 02:39:16 +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	QScript authors can now tag functions as intermediate. Functions tagged as intermediate will be skipped unless another function in the graph needs their output.	2010-10-18 22:11:14 +00:00
settings	Added status email support with -statusTo. Will send emails on failure of an individual function or success/failure of the whole pipeline.	2010-10-14 15:58:52 +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	Added status email support with -statusTo. Will send emails on failure of an individual function or success/failure of the whole pipeline.	2010-10-14 15:58:52 +00:00