zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
gatk3的最后一个经典版本3.8
4,303 Commits
1 Branch
0 Tags
257 MiB
Java 95.8%
Scala 3.8%
R 0.2%
JavaScript 0.1%
 
 
 
 
Go to file
chartl c355afc320 Queue now does job tracking (replace -run with -status in the command line). Produces output that looks like: 
INFO  20:58:17,827 QCommandLine - Checking pipeline status 
INFO  20:58:23,234 QGraph$$anonfun$formatStatus$1 - Height_Hirschhorn_NHGRI.uncleaned_MergeIndels [DONE] 
INFO  20:58:23,236 QGraph$$anonfun$formatStatus$1 - IndelGenotyper_158.bam [DONE] 5t/5d/0r/0p/0f 
INFO  20:58:23,237 QGraph$$anonfun$formatStatus$1 - IndelGenotyper_929.bam [DONE] 5t/5d/0r/0p/0f 
INFO  20:58:23,238 QGraph$$anonfun$formatStatus$1 - Height_Hirschhorn_NHGRI.uncleaned_SNP_calls [NOT DONE] 5t/0d/0r/5p/0f 
INFO  20:58:23,239 QGraph$$anonfun$formatStatus$1 - Height_Hirschhorn_NHGRI.uncleaned_HandFilter [NOT DONE] 
INFO  20:58:23,240 QGraph$$anonfun$formatStatus$1 - IndelGenotyper_1122.bam [DONE] 5t/5d/0r/0p/0f 
INFO  20:58:23,240 QGraph$$anonfun$formatStatus$1 - Height_Hirschhorn_NHGRI.uncleaned_VariantRecalibrator [NOT DONE] 
INFO  20:58:23,241 QGraph$$anonfun$formatStatus$1 - IndelGenotyper_913.bam [DONE] 5t/5d/0r/0p/0f 
INFO  20:58:23,242 QGraph$$anonfun$formatStatus$1 - IndelGenotyper_2037.bam [DONE] 5t/5d/0r/0p/0f 
INFO  20:58:23,243 QGraph$$anonfun$formatStatus$1 - Height_Hirschhorn_NHGRI.uncleaned_VariantEval [NOT DONE] 
INFO  20:58:23,244 QGraph$$anonfun$formatStatus$1 - Height_Hirschhorn_NHGRI.uncleaned_Cluster [NOT DONE] 
INFO  20:58:23,245 QGraph$$anonfun$formatStatus$1 - IndelGenotyper_106.bam [DONE] 5t/5d/0r/0p/0f 
INFO  20:58:23,246 QGraph$$anonfun$formatStatus$1 - Height_Hirschhorn_NHGRI.uncleaned_Cluster_and_Indel_filter [NOT DONE] 
INFO  20:58:23,247 QGraph$$anonfun$formatStatus$1 - Height_Hirschhorn_NHGRI.uncleaned_ApplyVariantCuts [NOT DONE] 
INFO  20:58:23,248 QGraph$$anonfun$formatStatus$1 - Height_Hirschhorn_NHGRI.uncleaned_GenomicAnnotator [NOT DONE] 
INFO  20:58:23,248 QGraph$$anonfun$formatStatus$1 - IndelGenotyper_1713.bam [DONE] 5t/5d/0r/0p/0f 




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4340 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-09-24 00:59:09 +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 Sliced the GAE in half like a gordian knot to avoid the constant merge conflicts. 2010-09-23 23:28:55 +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 Queue now does job tracking (replace -run with -status in the command line). Produces output that looks like: 2010-09-24 00:59:09 +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