My understanding was that query intervals of primary and supplementary alignments of the same read never overlap. But it looks like I'm mistaken, because they are overlapping...is there an option to force non-overlapping intervals?

$ minimap2 ref.fasta tiny.fasta --cs --secondary=no 2> /dev/null | cut -f 3,4,6,8,9
4378	16658	ENA|CP002685|CP002685.1:5190000-5210000	8050	20000
13615	22038	ENA|CP002685|CP002685.1:5190000-5210000	8174	15881

Data: Archive.zip

Thank you,
Armin