zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
3,798 Commits
1 Branch
0 Tags
257 MiB
Commit Graph

9 Commits (25a27b78bcfcbcfeb9e89e196af5ffbbfbc4efb3)

Author SHA1 Message Date
depristo 25a27b78bc 1KG Table 1 counting pipeline. Useful example 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3819 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-17 22:30:56 +00:00
depristo b0fc42906e Better DOT support and updated recalibration pipeline 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3811 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-16 20:54:51 +00:00
depristo 81eef0d993 DOT visualization with Queue. More sophisticated recalibation queue script with scatter/gather 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3799 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-15 22:32:48 +00:00
depristo 530a320f28 Intermediate commit of scatter/gather recalibation pipeline 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3785 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-13 22:46:08 +00:00
kshakir 1d399aa2f3 Added a temporary gatkLoggingLevel field to the soon to be obsolete GatkFunction while finishing up the delayed generic gatk walker utility. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3757 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-11 03:27:32 +00:00
kshakir 7be8c35eb2 Workaround for scala trait erasing parameterized types: 
- Requiring explicit @ClassType on parameterized fields in traits.
- Scatter / Gather functions are now abstract classes since @ClassType can't be used on parameterized fields with type parameters.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3726 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-07 03:15:10 +00:00
rpoplin 87470d5fe5 Checking in a simplistic VR qscript file for posterity's sake 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3705 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-01 18:53:17 +00:00
kshakir 894ad354fa Fixed typo in the name of the shell directory. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3644 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-25 20:59:40 +00:00
kshakir 75c98c42b8 Started path of deprecation of Sting's @Argument by splitting the annotation into @Output and @Input. Anything that's not an @Output should be an @Input. 
Checked in example qscripts that are basically todo integration tests.
Replaced use of queue @Input/@Output with Sting's new @Input/@Output.  This means you'll now have to doc-ument the annotations.
More work on dependency resolution cycles being created in the graph during scatter/gather.
Filtering nulls to avoid NPE exceptions in scala's 'Collection'.hashCode.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3643 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-25 20:51:13 +00:00