Closed kishwarshafin closed 5 years ago
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.
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. 👍
This should now be available in pypi and conda and well as the source on github.
Thank you so much!
No problem, thanks.
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:In this setup, if you look through the script, the mini_align under "trim" condition is missing
-m
parameter which ends up not generating anMD
tag in the alignment andref_seqs_from_bam
throws a ValueError sayingno 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?