Breakend orientation not output correctly

[amcpherson]

The code always outputs breakends with the same orientation:

minda/minda/ensemble.py

Line 201 in 182fbcf

return f"N]{row['#CHROM_y']}:{row['POS_y']}]"

Orientation of BND type breakpoints is thus lost after running minda and the resulting vcf is not compliant with the vcf format.

from the vcf format defined here: https://samtools.github.io/hts-specs/VCFv4.2.pdf

REF ALT Meaning
s t[p[ piece extending to the right of p is joined after t
s t]p] reverse comp piece extending left of p is joined after t
s ]p]t piece extending to the left of p is joined before t
s [p[t reverse comp piece extending right of p is joined before t

[mikolmogorov]

Thanks! This is an outstanding issue, @asherbryant did you have chance to look into that?

[apsteinberg]

Hello @mikolmogorov and @asherbryant,

I work with @amcpherson and had some time to edit minda to allow for this feature. I pushed some commits on the fork of your repo I have which is referenced in PR #14. I will add some additional comments there.

Thanks,
Asher

[mikolmogorov]

@apsteinberg thank you - we'll take a look shortly!