5815348ebc
Switch to newer version of comp tracks (and make the trigger track a comp as well). Indel cleaning should override the interval list and only use the contig interval list; and also force jobs to go to long.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3941 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-04 20:05:27 +00:00
9132c98eec
Slightly smarter interval list dealing (whole exome intervals are .interval_list, whole genome are .interval.list). Also use BTI with the Genomic Annotator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3904 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-29 22:04:02 +00:00
54d93f63d2
Hacky fix for LSF confusion -- submitted jobs check to see if their directory exists, despite depending on the job which creates said directory. Filter strings now have escaped quotes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3903 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-29 21:35:50 +00:00
0f9baa2e94
Ha ha ha ha ha
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:(
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3902 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-29 20:48:35 +00:00
7a5ee485d2
Full pipeline now works through DAG creation. First draft; more work to do to make it cleaner and better command-line input handling (and properties handling); but the DAG is rendered and looks good.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3898 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-29 19:36:17 +00:00
4d4cf6e1dc
Updates to calling pipeline
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3896 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-29 18:37:20 +00:00
62a9217a61
A brute-force exome/genome independent end-to-end cleaning/calling pipeline using Queue
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3894 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-29 13:17:14 +00:00
25a27b78bc
1KG Table 1 counting pipeline. Useful example
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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
b0fc42906e
Better DOT support and updated recalibration pipeline
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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
81eef0d993
DOT visualization with Queue. More sophisticated recalibation queue script with scatter/gather
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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
530a320f28
Intermediate commit of scatter/gather recalibation pipeline
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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
1d399aa2f3
Added a temporary gatkLoggingLevel field to the soon to be obsolete GatkFunction while finishing up the delayed generic gatk walker utility.
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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
7be8c35eb2
Workaround for scala trait erasing parameterized types:
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- 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
87470d5fe5
Checking in a simplistic VR qscript file for posterity's sake
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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
894ad354fa
Fixed typo in the name of the shell directory.
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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
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.
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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
chartl
depristo
kshakir
rpoplin