gatk3的最后一个经典版本3.8

corin 3ec0e09edd ADPR is now included in the full calling pipeline. The most up to date version of the ADPR is about to be committed and should be used with the script for now. The qscript now calls for two additional strings as inputs: the sequencing machines used and the sequencing protocol. In order for ADPR to finish successfully, a squid file for both the lane and sample level data needs to be produced, reformatted and named <projectBase>_lanes.txt or <projectBase>_samps.txt, respectively. These files need to be in the working directory. When database access is ready, this and the protocol and sequencer parameters of the r script will go away. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4345 348d0f76-0448-11de-a6fe-93d51630548a		2010-09-24 19:28:43 +00:00
R	This is an updated version of the automated data processing report. Each page in the report is a stand alone function, which are linked together with a function which pulls all appropriate data (assuming a standard naming convention) and generates the pdf. This script still need to respond appropriately when it doesn't find the data it needs, database access, and a way of getting some information from sequencing for the tearsheet.	2010-09-23 18:08:16 +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	GATK now detects and UserExceptions when human lexicographically sorted data is provided	2010-09-24 15:19:48 +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	Fix for DoC issue with multiplexer -- will retire use of multiplexer when	2010-09-07 00:44:07 +00:00
perl	- Update DoC to support output to /dev/null.	2010-09-08 23:43:18 +00:00
python	Do this the right way	2010-09-19 04:30:48 +00:00
ruby	accidentally commited an old tool	2010-08-25 15:42:02 +00:00
scala	ADPR is now included in the full calling pipeline. The most up to date version of the ADPR is about to be committed and should be used with the script for now. The qscript now calls for two additional strings as inputs: the sequencing machines used and the sequencing protocol. In order for ADPR to finish successfully, a squid file for both the lane and sample level data needs to be produced, reformatted and named <projectBase>_lanes.txt or <projectBase>_samps.txt, respectively. These files need to be in the working directory. When database access is ready, this and the protocol and sequencer parameters of the r script will go away.	2010-09-24 19:28:43 +00:00
settings	The battle is over. Picard is revved.	2010-09-03 05:28:01 +00:00
shell	Updated from SnakeYAML 1.6 to 1.7.	2010-09-22 19:47:49 +00:00
testdata	and add changes to the vcf used in testing	2010-06-25 02:56:02 +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	Added the new pipeline classes to the StingUtils.jar so that ant test picks them up.	2010-09-22 20:05:22 +00:00
ivy.xml	Updated from SnakeYAML 1.6 to 1.7.	2010-09-22 19:47:49 +00:00