chartl
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5815348ebc
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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.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3941 348d0f76-0448-11de-a6fe-93d51630548a
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2010-08-04 20:05:27 +00:00 |
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chartl
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9132c98eec
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Slightly smarter interval list dealing (whole exome intervals are .interval_list, whole genome are .interval.list). Also use BTI with the Genomic Annotator
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3904 348d0f76-0448-11de-a6fe-93d51630548a
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2010-07-29 22:04:02 +00:00 |
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chartl
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54d93f63d2
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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.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3903 348d0f76-0448-11de-a6fe-93d51630548a
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2010-07-29 21:35:50 +00:00 |
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chartl
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0f9baa2e94
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Ha ha ha ha ha
:(
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3902 348d0f76-0448-11de-a6fe-93d51630548a
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2010-07-29 20:48:35 +00:00 |
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chartl
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7a5ee485d2
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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.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3898 348d0f76-0448-11de-a6fe-93d51630548a
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2010-07-29 19:36:17 +00:00 |
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chartl
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4d4cf6e1dc
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Updates to calling pipeline
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3896 348d0f76-0448-11de-a6fe-93d51630548a
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2010-07-29 18:37:20 +00:00 |
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chartl
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62a9217a61
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A brute-force exome/genome independent end-to-end cleaning/calling pipeline using Queue
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3894 348d0f76-0448-11de-a6fe-93d51630548a
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2010-07-29 13:17:14 +00:00 |