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open2c / pairtools

Extract 3D contacts (.pairs) from sequencing alignments
MIT License
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list index out of range error on line 574 of pairtools_parse.py #77

Closed nkschaefer closed 5 years ago

nkschaefer commented 5 years ago

Hi,

I'm not an expert on the code, but I'm getting a fatal list index out of range error thrown by the parse_sams_into_pair function in pairtools_parse.py (line 574) -- the cause looks like trying to access the first element in algns1 and algns2, but my algns2 is empty in this case. I haven't dug deep enough to know if this is due to a problem with my BAM file and how it was generated, or whether the program should check for and handle this (or print some kind of error message).

I tried adding a check that len(sams1) > 0 and len(sams2) > 0 on line 782, in streaming_classify, and this lets the program run without the error. No idea if this will cause any other problems downstream, though.

Thanks for any help you can provide.

--Nathan

nkschaefer commented 5 years ago

It looks like this was a problem with how the data were generated upstream.

golobor commented 5 years ago

apologies for not answering earlier - I've been busy moving my family across continents. Glad to hear that it got resolved!

On Tue, 24 Sep 2019 at 23:30, nkschaefer notifications@github.com wrote:

Closed #77 https://github.com/mirnylab/pairtools/issues/77.

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