Raise error if bam index is missing

katerinakazantseva / strainy

Graph-based assembly phasing

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Raise error if bam index is missing #3

Closed mikolmogorov closed 1 year ago

mikolmogorov commented 1 year ago

Fail early and output meaningful error message if bam index is missing. Currently the pipeline continues and produces more cryptic errors.

katerinakazantseva commented 1 year ago

done Traceback (most recent call last): File "/Users/ekaterina.kazantseva/metaPhase/metaPhase.phase.py", line 2, in from params import * File "/Users/ekaterina.kazantseva/metaPhase/params.py", line 35, in raise Exception("No index file found (%s) Please create index using \"samtools index\"." % bam_index) Exception: No index file found (/Users/ekaterina.kazantseva/MT/5strain_hifi_sim/minigraph/minigraph.bam.bai) Please create index using "samtools index".