pomoxis assess assembly `-T` parameter without `-b` gives an error.

[kishwarshafin]

Hello,

I've been using the assess assembly module, and it's really helpful. But I am having an issue running it with -T and without a bed file parameter. My intended use is:

assess_assembly \
-i <input_fasta> \
-r <ref_fasta> \ 
-t <threads> \
-p <output_prefix> \
-T 

In this setup, if you look through the script, the mini_align under "trim" condition is missing -m parameter which ends up not generating an MD tag in the alignment and ref_seqs_from_bam throws a ValueError saying no MD tag found. If I enable -C or edit the script to have -m in mini_align that fixes the problem, is my intended use not correct? I generated a bed file with all the segments of primary alignment, and it gives the same result. So, there may need to be a fix?

[cjw85]

Hi @kishwarshafin,

This looks like it may be an unhandled case. This week is naturally a busy week for us with London Calling next week. We will have a look at this at the first opportunity.

[kishwarshafin]

Good to know. I understand, I am also using this for London Calling :-). No worries, I have a fix. Just wanted to be sure that this is an unhandled case not an unintended use of the analysis pipeline. Thanks for the quick reply. 👍

[cjw85]

This should now be available in pypi and conda and well as the source on github.

[kishwarshafin]

Thank you so much!

[cjw85]

No problem, thanks.