n variable not defined when running --first

[kjurdzinski]

I installed PMDtools with bioconda.

I prepare the table for plotting the DNA damage patterns, running:

samtools view mybam.bam | python pmdtools.0.60.py --platypus --requirebaseq 30

and get the error:

line 1074, in <module>
if n>0:
^
NameError: name 'n' is not defined

It seems the n variable is not defined in the script. I've got to fix it by adding:

n = firstC + firstT

just before line 1074 (i.e., as a new line 1074).