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BrooksLabUCSC / flair

Full-Length Alternative Isoform analysis of RNA
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flair correct crash with AttributeError: 'bool' object has no attribute 'find_overlap' #290

Closed diekhans closed 10 months ago

diekhans commented 10 months ago 
 python ../flair/flair.py correct --query flair.aligned.bed --genome ../refs/GRCh38.primary_assembly.genome.fa --gtf ../refs/gencode.v43.primary_assembly.annotation.gtf --shortread ../refs/H0.introns.bed --threads 32 --print_check

How did you install Flair? github, commit f94f95b00fc35dd4dda0aeffd1c63552bb89c70b

What happened?

AttributeError: 'bool' object has no attribute 'find_overlap'

see attached along for full stack

correct.log We know it's ugly but we promise it helps us solve problems faster.

What else do we need to know? This happens on chromosome GL000218.1, which has only 370 alignments.

I can share example data or test.

diekhans commented 10 months ago

turns out this happens when there is a chromosome where there is no short-read junctions mapped to it. Minimal test case attched

no-juncs-bug.tar.gz