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
3,519 Commits
1 Branch
0 Tags
257 MiB
Java 95.8%
Scala 3.8%
R 0.2%
JavaScript 0.1%
 
 
 
 
Go to file
hanna c3b68cc58d Rethinking DownsamplingLocusIteratorByState with a flattened read structure. Samples are kept 
independent while processing, and only merged back in a priority queue if necessary in a special
variant of the ReadBackedPileup.  This code is not live yet except in the case of naive deduping.
Downsampling by sample temporarily disabled, and the ReadBackedPileup variant is sketchy and
not well integrated with StratifiedAlignmentContext or the walkers.  Cleanup to follow.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3540 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-06-13 01:47:02 +00:00
R Automatic cutting of recalibrated variant calls using ApplyVariantCuts. VariantRecalibrator produces the tranches plot alongside the optimization curve. Specify the levels using -tranche 1.0 -tranche 5.0 etc 2010-06-02 15:03:00 +00:00
archive Retiring multi-sample genotyper 2010-05-20 14:11:11 +00:00
c Reduce file handle usage. 2010-01-05 18:03:01 +00:00
doc moved to wiki 2009-07-22 16:35:23 +00:00
java Rethinking DownsamplingLocusIteratorByState with a flattened read structure. Samples are kept 2010-06-13 01:47:02 +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 Update to the latest rev of the picard sharding patch. Includes updates reflecting 2010-06-06 20:33:21 +00:00
perl A script to sanity check that a release is runnable. 2010-05-26 17:45:42 +00:00
python Added both inclusive and exclusive filters 2010-06-11 18:40:41 +00:00
ruby Adding the ruby directory, and a simple script to restart Bamboo 2009-12-03 22:48:48 +00:00
scala/src Multiple inputs / outputs for rules. 2010-05-30 08:28:16 +00:00
settings Fixing a VCF bug for Sendu: we weren't emitting flags (booleans) correctly in VCF3.3 (rev'ed tribble for this). 2010-06-11 16:42:06 +00:00
shell Renaming error to getNegLog10PError(); added Cached clearing method to GL; SSG now has a CallResult that counts calls; No more Adding class to System.out, now to logger.info; First major testing piece (and general approach too) to unit testing of a walker -- SingleSampleGenotyper now knows how many calls to make on a particular 1mb region on NA12878 for each call type and counts the number of calls *AND* the compares the geli MD5 sum to the expected one! 2009-09-04 12:39:06 +00:00
testdata a small dbsnp file for Tribble testing 2010-02-18 18:12:55 +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 Removing these utilities as part of a hostage negotation with Matt. Can I have my journal club paper now?! 2010-06-11 21:41:29 +00:00
ivy.xml JEXL2 upgrade. Improvements to JEXL processing including dynamically resolving variable -> value bindings instead of up front adding them to a map. Performance improvements and code cleanup throughout. 2010-06-07 00:33:02 +00:00