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brentp / bwa-meth

fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
https://arxiv.org/abs/1401.1129
MIT License
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Fixed bug in argument checking which meant that only indexing ran #73

Closed chris-cheshire closed 3 years ago

chris-cheshire commented 3 years ago

I ran this at the latest commit, its looks like the alignment code cannot be reached due to the following lines: 

if len(args) > 0:
    assert len(args) == 2, ("must specify fasta as 2nd argument")

The main alignment parameters do not pass this check and always error out with "must specify fasta as 2nd argument".

I have fixed argument checking so this runs properly.

brentp commented 3 years ago

Thanks @chris-cheshire @PoisonAlien can you comment on this?

PoisonAlien commented 3 years ago

@brentp Yes, I can reproduce the error. Thank you @chris-cheshire for the fix, it works.

I also apologize for the mistake, I should have been more careful and double checked.

brentp commented 3 years ago

Thanks @chris-cheshire for finding and fixing. And thanks @PoisonAlien for checking, no problem on the mistake.