for _, l := range c {
if alpha.IsValid(l) {
w[alpha.IndexOf(l)]++
}
}
var max, maxi int
for i, v := range w {
if v > max {
max, maxi = v, i
}
}
return alphabet.QLetter{
L: alpha.Letter(maxi),
Q: alphabet.Ephred(1 - (float64(max) / float64(len(c)))),
}
}
// A default ConsenseFunc function that takes letter quality into account.
// http://staden.sourceforge.net/manual/gap4_unix_120.html
DefaultQConsensus ConsenseFunc = func(a Aligned, alpha alphabet.Alphabet, pos int, fill bool) alphabet.QLetter {
w := make([]float64, alpha.Len())
for i := range w {
w[i] = 1
}
others := float64(alpha.Len() - 1)
c := a.ColumnQL(pos, fill)
for _, l := range c {
if alpha.IsValid(l.L) {
// SetE sets the quality at position pos to e to reflect the given p(Error).
func (s *QSeq) SetE(i int, e float64) error {
s.Seq[i-s.Offset].Q = alphabet.Ephred(e)
return nil
}