AvA of ONT reads

[diego-rt]

Hey there,

A few issues we spotted when testing out wfmash for AvA:

Example command:

wfmash -t 16 -s 1000 -c 2k -l 4k -P inf -X -H 0 -f ont_reads.fastq ont_reads.fastq > aln.paf

1. When performing self-alignments, alignments are only output in one direction: query -> target but not in the other target -> query.
2. Omitting the -X option leads to a huge unexplained decline in the number of alignments being output. (7279 alignments without -X vs 172888 with -X)
3. We were wondering whether indels are left-aligned in the CIGAR and whether they would be both left-aligned in the forward and reverse alignments. Further context here:

nanoporetech/dorado#851 (comment)

All tests were carried out using the latest commit on the main branch.

Many thanks!