gatk3的最后一个经典版本3.8

depristo 0e062ae040 V1 of the data processing paper, produced results for the manuscript we presented. Commit for archival purposes ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4648 348d0f76-0448-11de-a6fe-93d51630548a		2010-11-11 01:43:21 +00:00
R	now prints a nice report, can be invoked from command line	2010-11-09 19:44:10 +00:00
archive	Fisher exact makes a return. Seems to be working properly. Current tagged as a work in progress. Needs to take the filtered context to be truly correct.	2010-10-22 20:35:53 +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	Improvement in exact allele frequency calculation model (still under test, but this is definitely better than what I had before). Instead of approximating log(10^x+10^y) as max(x,y), approximate full Jacobian formula max(x,y)+log(1+10^-abs(x-y)) with static lookup table for the second term.	2010-11-11 01:22:35 +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	by request, an indexer tool to create Tribble style indexes outside of the GATK	2010-11-06 18:59:06 +00:00
perl	Also removed contig intervals from the pipeline sanity check perl scsript.	2010-10-21 11:23:34 +00:00
python	V1 of the data processing paper, produced results for the manuscript we presented. Commit for archival purposes	2010-11-11 01:43:21 +00:00
ruby	accidentally commited an old tool	2010-08-25 15:42:02 +00:00
scala	Moving all file cleanup to IOUtils for easier debugging.	2010-11-10 21:00:58 +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	GSA-413 Explicitly set all compilers to use 512m memory maximum instead of 64m default maximum and running them out of the ant process.	2010-11-09 19:32:19 +00:00
ivy.xml	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00