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zstephens / neat-genreads

NEAT read simulation tools
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Bam input into compute_fraglen.py measures read length rather than insert size #91

Closed jeffpbruce closed 3 years ago

jeffpbruce commented 3 years ago

Describe the bug If a bam file is input directly into compute_fraglen.py without prior conversion to a .sam, the output pickle file appears to contain a model describing the read length rather than the insert size. I used this method because the command described in the readme (./samtools view toy.bam | python compute_fraglen.py) yielded the following error:

usage: compute_fraglen.py [-h] -i input -o output
compute_fraglen.py: error: the following arguments are required: -i, -o

To Reproduce python compute_fraglen.py -i file.bam -o fraglen

Expected behavior A a model of the insert size. What we receive instead is a model of the read length.

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joshfactorial commented 3 years ago

You're correct that the readme was incorrect. I have updated that. We're shifting the NEAT repository to an NCSA owned repo, which you can find here: https://github.com/ncsa/neat-genreads/issues/1. I recreated this issue there and will work on solving it there.