NAME

       last-map-probs - Add extra column with mapping probabilities

SYNOPSIS

       last-map-probs [options] lastal-alignments

DESCRIPTION

       Calculate  a  mismap  probability  for  each  alignment.  This is the probability that the
       alignment does not reflect the origin of the query sequence, assuming  that  one  reported
       alignment does reflect the origin of each query.

OPTIONS

       -h, --help
              show this help message and exit

       -m M, --mismap=M
              don't write alignments with mismap probability > M (default: 0.01)

       -s S, --score=S
              don't write alignments with score < S (default: e+t*ln[1000])