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5 Commits (cd38dfb4ef8a0043ccad553e4eae6ddebf165e47)

Author SHA1 Message Date
kiran 4f83151c4e Evaluates within standard target and expanded target separately. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5268 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-17 23:04:24 +00:00
kshakir a189454343 FCP only adds the expand intervals QFunction once per script instead of once per QFunction using the ExpandTargets scala trait. 
Eval dbSNP's type now based on eval dbSNP instead of genotype dbSNP.
Using an external treemap instead of the JGraphT internal node set to speed up larger graph generation.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5261 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-17 19:09:03 +00:00
kiran c0a4af3809 Expands targets by 50-bp on both sides when the expandIntervals argument is greater than 0. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5251 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-16 14:47:52 +00:00
corin d2efea6003 This is a draft of the improved and prettified pipeline. It may not yet compile, but Kiran is taking over adding a few more things as I finish up other tasks. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5248 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-15 19:35:00 +00:00
kshakir 8040998c15 Renamed the pipeline yaml dbsnpFile to genotypeDbsnp, and added an evalDbsnp. 
Added a genotypeDbsnpType and evalDbsnpType to check the extensions for .vcf or .rod.
Moved renaming of "recalibrated" bams to "cleaned" from sed to yaml generation template (see diff for more info).
Renamed fCP.q to FCP.q.
Though it's still disabled until VariantEval is updated, added changes above to the FCPTest.
Removed refseq table from the queue.sh wrapper script. Only specified in the yaml.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5213 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-07 22:01:09 +00:00