Open ameynert opened 5 days ago
The three valid scenarios for hits being returned from bwa aln
are:
HN = 0
, there should be no XA
tags returned, and thus hits = []
0 < HN <= max_hits
. HN = n
, where n
is the number of hits, and len(hits) == n
HN > max_hits
. HN = n
, where n
is the number of hits, and hits = []
because although the primary hit is returned, there are no XA
tags representing the alternate reads, so we return none of them.
bwa aln
sometimes returns a read that is unmapped but does have hits (both primary andXA
tag). Suggest that we ignore this case: