vcf_out may be unbound in sniffles v2.3.2

[MikkelSchubert]

If --vcf is not set on the command-line, then the vcf_out variable is unbound at

Sniffles/src/sniffles/sniffles

Line 447 in d2d3bfd

t.result.emit(vcf_out=vcf_out, snf_out=snf_out, **rkwargs)

I'm guessing that the fix is just to add vcf_out = None before

Sniffles/src/sniffles/sniffles

Line 190 in d2d3bfd

if config.vcf is not None:

Output:

2024-04-22 13:02:36,811 INFO sniffles.main (1575379): Used command: sniffles --threads 8 --reference resources/genome.fa --input input.bam --snf output.snf --tandem-repeats human_GRCh38_no_alt_analysis_set.trf.bed
[snip]
2024-04-22 13:04:29,601 INFO sniffles.main (1575379): Took 110.51s.
2024-04-22 13:04:29,601 INFO sniffles.main (1575379): 
Traceback (most recent call last):
  File "/opt/software/sniffles/2.3.2/bin/sniffles", line 511, in <module>
    Sniffles2_Main(processes)
  File "/opt/software/sniffles/2.3.2/bin/sniffles", line 447, in Sniffles2_Main
    t.result.emit(vcf_out=vcf_out, snf_out=snf_out, **rkwargs)
UnboundLocalError: cannot access local variable 'vcf_out' where it is not associated with a value

[hermannromanek]

Hi @MikkelSchubert ,

Thanks for reporting this, you are right - I just pushed a fix containing your suggestion.

Thanks,
Hermann

[lfpaulin]

Fixed in 48b9645