Unexpected alignments

[jdidion]

Attached is a single read from Simpson et al. '23. The vector sequence is also attached, as well as the alignments in SAM format. There are two unexpected things about these alignments:

1. There are 11 reads but only 1 is marked supplementary. The other 10 are neither secondary nor supplementary. (I am using feat-44-sam-flags-and-tags branch).
2. Several of the alignments are contiguous without gaps - these should be a single alignment.

test_data.tgz

[jdidion]

For reference, here are the minimap2 alignments (to the mouse genome + vector sequences)
minimap_test.sam.gz

[nh13]

Fixed in c6bd79f

Also, here's some settings that penalize the jumps a bit more, which seems to make a difference.

	--jump-score-same-contig-and-strand -40 \
	--jump-score-same-contig-opposite-strand -80 \
	--jump-score-inter-contig -160 \

Let me know if this works for you and we can close this issue.

[nh13]

Perhaps we should change the defaults in the tool as well?

[jdidion]

Yes, the commit fixes the flags issue, and those parameters fix the split alignment issue.

I like the idea of tuning the jump parameters individually (right now all are set to -10), but maybe we should see a few more cases before deciding. I'll open a separate tracking issue for that.