depristo
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588006ee92
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Now supports strings in command line for farm submission
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2507 348d0f76-0448-11de-a6fe-93d51630548a
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2010-01-06 13:15:40 +00:00 |
andrewk
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7eb21e55c1
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Added die_on_fail which outputs an error message and stops execution if a farm or terminal command fails
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1618 348d0f76-0448-11de-a6fe-93d51630548a
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2009-09-14 23:30:13 +00:00 |
ebanks
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8c33dd2393
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enable job names
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1582 348d0f76-0448-11de-a6fe-93d51630548a
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2009-09-11 13:08:53 +00:00 |
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depristo
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d665d9714f
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By default now writes output to JOBID.lsf.output instead of going to email -- based on recommendations from the cancer group
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1325 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-28 13:18:58 +00:00 |
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depristo
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f5b00c20d0
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Updated python files
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1182 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-07 14:15:39 +00:00 |
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depristo
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8ac40e8e2d
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Updated version of the recalibration tool
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1060 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-19 17:45:47 +00:00 |
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depristo
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819862e04e
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major restructuring of generalized variant analysis framework. Now trivally easy to add additional analyses. Easy partitioning of all analyses by features, such as singleton status. Now has transition/transversional bias, counting, dbSNP coverage, HWE violation, selecting of variants by presence/absense in dbs. Also restructured the ROD system to make it easier to add tracks. Also, added the interval track -- if you provide an interval list, then the system autoatmically makese this available to you as a bound rod -- you can always find out where you are in the interval at every site. Python scripts improved to handle more merging, etc, into population snps.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@918 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-05 23:34:37 +00:00 |
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depristo
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3998085e4b
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more and better python scripts for dealing with calls
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@881 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-02 20:37:19 +00:00 |
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depristo
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c72601322a
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now returns the farm id when submitting a job!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@825 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-26 22:23:24 +00:00 |
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depristo
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04e51c8d1d
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Better version of MergeBAMBatch -- more options for creating the file
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@787 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-21 22:26:19 +00:00 |
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depristo
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3b1f84e15b
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Slightly improved interface to merging utility for multiple bam files
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@757 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-20 12:54:41 +00:00 |
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depristo
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2eabcfedb7
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Fixed potential bug with next() operation returning empty contexts when a read contains a large deletion. We can now use the look ahead safely...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@439 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-15 21:41:30 +00:00 |
hanna
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2ee2623926
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Move non-java code out of playground.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@154 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-23 19:31:38 +00:00 |
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hanna
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5031875507
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Move to new directory organization.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@35 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-11 20:58:01 +00:00 |
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depristo
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17aabb38f9
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Basic reorganization of tree
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@8 348d0f76-0448-11de-a6fe-93d51630548a
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2009-02-28 15:28:56 +00:00 |