Name in report do not match the reference name (-r)

jonas-fuchs / BAMdash

create a interactive coverage plot dashboard from bam files and add gb, vcf and bed tracks

GNU General Public License v3.0

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Name in report do not match the reference name (-r) #19

Closed KristinaGagalova closed 3 months ago

KristinaGagalova commented 3 months ago

Hi,

I am running the following, on the bamdash version 0.3, installed through pip:

bamdash -r tig00000043 -b 19Ptm93.lr.sort.bam --dump -q 0

The output (html and dump text) does not show the reference name I used. The length of the sequence looks correct, though, so it may be an error in the output/name parsing. Capture30

Could you please take a look?

Thank you in advance

jonas-fuchs commented 3 months ago

Hi Kristina,

thanks for the feedback. You actually found a quite big bug that was in here a while. The statistics for reference, mapped and unmapped are apparently not correct (it always uses the first index). Should be an easy fix but something you never notice until you use this tool for bams mapped to multiple references. I will fix this ASAP! Sry for the inconvenience, but it might be that mapped/unmapped and reference are at the moment not necessarily correct.

Cheers, Jonas

jonas-fuchs commented 3 months ago

Fix was quite easy. I will double check everything and release 0.3.1 ;)

jonas-fuchs commented 3 months ago

Should be fixed now with 0.3.1. Thanks again for the feedback!

KristinaGagalova commented 3 months ago

It's correct now! Thank you for the fast fis, I am planning to use this great tool for my pipeline :)