func isSecondary(r *boom.Record) bool {
seq := r.Seq()
if len(seq) < 10 {
return false
}
if r.Flags()&boom.Reverse == 0 {
return seq[9]|' ' == 'a'
}
return seq[len(seq)-10]|' ' == 't'
}
func isPrimary(r *boom.Record) bool {
seq := r.Seq()
if len(seq) < 1 {
return false
}
if r.Flags()&boom.Reverse == 0 {
return seq[0]|' ' == 't'
}
return seq[len(seq)-1]|' ' == 'a'
}
func qualOk(r *boom.Record, minId, minQ int, minAvQ float64) (ok bool) {
var (
off, l int
match int
mQ int
edit int
)
for _, t := range r.Tags() {
if t.Tag() == [2]byte{'N', 'M'} {
switch e := t.Value().(type) {
case byte:
edit = int(e)
case uint16:
edit = int(e)
case uint32:
edit = int(e)
default:
edit = 0
}
}
}
cigar := r.Cigar()
qual := r.Quality()
for _, c := range cigar {
t := c.Type()
if t == boom.CigarMatch || t == boom.CigarInsertion || t == boom.CigarSoftClipped || t == boom.CigarEqual || t == boom.CigarMismatch {
off = l
l += c.Len()
for _, q := range qual[off:l] {
if int(q) < minQ {
return false
}
if t == boom.CigarMatch || t == boom.CigarEqual {
match++
mQ += int(q)
}
}
}
}
match -= edit
ok = match*100 >= minId*l && mQ >= int(minAvQ*float64(l))
return
}
