Mappy fails when using MD tag

[tprodanov]

Here you can find two sequences. If you align them directly using minimap2

minimap2 -ax asm20 1.fa 2.fa --MD -o test.sam

it works without problems.

If you run it in mappy, specifically with preset='asm20' and with MD=True, it fails with segmentation fault.

import mappy

def load_seq(filename):
    with open(filename) as inp:
        next(inp)
        return ''.join(map(str.strip, inp))

seq1 = load_seq('1.fa')
seq2 = load_seq('2.fa')

aln = mappy.Aligner(seq=seq1, preset='asm20')
list(aln.map(seq=seq2))
print('It worked (1)')
list(aln.map(seq=seq2, MD=True))
print('It worked (2)')

will give

It worked (1)
[1]    16112 segmentation fault (core dumped)  ./test.py