[Mapass-help] Getting all hits for reads

[David H. S. <dhs@u.washington.edu>]

Heng,

I would like to get ALL the best hits for each read, but the 'mapview'
function and '-N' option only seem to return one best hit. Is there a
way to get mapass2 to give me all of the matching positions for each
read that have the best score (eg, all the hits for a read that matches 
an exact repeat in the genome). Thanks!

David Spencer

University of Washington
Dept. of Genome Sciences
Seattle, WA