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GMOD / jblast-jbconnect-hook

JBrowse/Galaxy-Blast Plugin
http://jblast.readthedocs.io
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JBlast only returns BLAST results of active chromosome #285

Closed EtienneBucher closed 4 years ago

EtienneBucher commented 4 years ago

Is there a way to get all BLAST hits instead of only for the active chromosome? I can see that the blastxml file contains all hits, but they are somehow filtered to the active chromosome in table.jason. Indeed the filtersettings.json file contains the contig information: {"contig":"Fvb1","score":{"type":"abs","min":159,"max":6315,"val":159},"evalue":{"type":"exp","min":0,"max":5.35731e-37,"val":5.35731e-37},"identity":{"type":"pct","min":77,"max":100,"val":77},"gaps":{"type":"pct","min":0,"max":12,"val":12}}

Best wishes, Etienne

EtienneBucher commented 4 years ago

I found a solution to this problem: In the global.js file one has to replace "Hit_accession" with "Hit_def" as follows: dataSet: { ChineseSpring: { path: 'IWGSC', featureMapping: 'hit', contigHandler(hit) { console.log("IWGSC contigHandler"); return hit.Hit_def; }, }, },