pairtools parse2 returns <class 'NotImplementedType'> when using --add-columns seq

[bskubi]

Hello!

I'm attempting to extract the seq fields from a bam file using pairtools parse2 by passing --add-columns 'seq'. It is returning the string <class 'NotImplementedType'> in all rows for the seq1 and seq2 columns of the output .pairs file, with the other columns looking normal. To try to debug, I modified the parse2 code to print sam.seq and sam.query_sequence on this line:

    if store_seq:
        print(sam.seq) # Also prints "<class 'NotImplementedType'>"
        algn["seq"] = sam.seq

This displays the same thing. I can extract the sequence from the sam fields instead, but it would be convenient to have it returned directly. Thanks for any help you can offer.

I'm using:
python 3.12, pysam 0.23.3, gcc/14.2.0, pairtools 1.1.2