I found sequences in generated maf are reversed for - reads. It looks the current code flips sequences when mut.seq_strand == '-', which is not needed as the maf_seq and read_seq are already in their correct direction and we compose maf alignment records with reference-side sequences in + direction.
I found sequences in generated maf are reversed for
-reads. It looks the current code flips sequences whenmut.seq_strand == '-', which is not needed as themaf_seqandread_seqare already in their correct direction and we compose maf alignment records with reference-side sequences in+direction.