func (d *DiversityFilter) Diff(r *sam.Record, genome []byte) (diff, length int) {
start := r.Start()
end := r.End()
if start < 0 || end > len(genome) {
if *debug {
text, err := r.MarshalSAM(sam.FlagDecimal)
raiseError(err)
log.Printf("acc: %s, genome length %d, read starts at %d and ends at %d: %s\n", r.Ref.Name(), len(genome), start, end, text)
}
length = 0
return
}
refSeq := genome[start:end]
diff = 0
read := map2Ref(r)
length = len(read)
for i := 0; i < length; i++ {
if read[i] != refSeq[i] {
diff++
}
}
return
}
