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JetBrains-Research / jbr

JBR Genome Browser
https://doi.org/10.1093/bioinformatics/btab376
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Detailed information at bed location perfomance could be improved #237

Closed iromeo closed 1 year ago

iromeo commented 1 year ago

Current implementation uses getBedEntryDescriptionFromLocation that uses processBed which was designed for preprocessing and scrores recalculation. Initially BedParser reads bed file using BedEntry it is lightweight version containing only location related info (chr, start, end). To find suitable bed records it is ok just to read & check BedEntry and then only parse rest fields in the found record. Instead getBedEntryDescriptionFromLocation actually parses every BedEntry to ExtendedBedEntry which is just time wasting for record lookup task.

iromeo commented 1 year ago

The problem exists for Bed and Filtered track views. Also need to check that in BigBed or Indexed track views there is no such issue.