search

GMOD / jbrowse

JBrowse 1, a full-featured genome browser built with JavaScript and HTML5. For JBrowse 2, see https://github.com/GMOD/jbrowse-components.
http://jbrowse.org
Other
464 stars 199 forks source link

Feature Request display CIGAR mismatch codes when zoomed out more #1643

Open childers opened 1 year ago

childers commented 1 year ago

Hi all,

we just encountered an issue where we can see the CIGAR mistmatches in an alignment track, but not when it is set to alignment2. I am not sure if this is a configurable option, and if so, what the name would be to override the default.

Ideally, the zoom level for showing these mismatches would be the same for Alignments2 features as it is for Alignments type features.

cmdcolin commented 1 year ago

if you want to consider hand editing the source code, you can remove or increase this check here which would conditionally display bpPerPx at different scales

https://github.com/GMOD/jbrowse/blob/master/src/JBrowse/View/FeatureGlyph/Alignment.js#L72-L78

The 'scale' is 1/bpPerPx so that would be 1/0.2=5 base pairs per pixel, then it stops displaying the mismatches currently. would be a longer process to make this change on our end e.g. releasing a whole new version of jbrowse, but it should be possible to make custom jbrowse builds with your custom changes