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elsiklab / multivariantviewer

A JBrowse plugin with a custom variant track for multi-VCF files and optionally plotting LD scores
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LDtrack shows error (invalid start and end coordinates) #21

Closed romens96 closed 5 years ago

romens96 commented 5 years ago

When running ldtrack I got an error when displaying the track . (Error: invalid start and end coordinates. must be provided, start must be less than or equal to end).

From what I checked in the example vcf files (volvox), there is only position column but not start and stop column. And from my understanding, only a position column is available in vcf files. Anyone had this error and solved it?

P.S I am new to this

cmdcolin commented 5 years ago

I believe there are some issues with the latest version of JBrowse that have not been fixed for both the Matrix and LDTrack types

I can update you when these become fixed

cmdcolin commented 5 years ago

By Latest version of JBrowse I mean anything after 1.16.0 version. You could try an earlier version to test also

cmdcolin commented 5 years ago

Ok, the code should be updated on this repo to work better with JBrowse 1.16.0+. Pull from master or get the latest version from the releases page :)

cmdcolin commented 5 years ago

Let me know if there are any issues

romens96 commented 5 years ago

Let me know if there are any issues

@cmdcolin Thank you for your quick assistance. Really appreciate it. Will let you know if there are still issues. Thanks again!