biostars 173201

answer.py

from simplesam import Reader
from pyfaidx import Fasta

with Reader(open('library.bam', 'r')) as sam_file, Fasta('hg38.fa', as_raw=True) as hg38:
  for read in sam_file:
    if read.mapped:  
      # might also want to handle read.reverse here
      prior_pos = read.pos - 2  # read.pos is 1-based
      prior_base = hg38[read.rname][prior_pos]