// Set the quality at position pos to e to reflect the given p(Error).
func (self *QSeq) SetE(pos seq.Position, e float64) {
if pos.Ind != 0 {
panic("packed: index out of range")
}
self.S[pos.Pos-self.offset] &^= ((1 << 6) - 1) << 2
self.S[pos.Pos-self.offset] = alphabet.QPack(alphabet.Ephred(e)) << 2
}
// Set the quality at position pos to l to reflect the given p(Error).
func (self *QSeq) SetE(pos seq.Position, e float64) {
if pos.Ind != 0 {
panic("protein: index out of range")
}
self.S[pos.Pos-self.offset].Q = alphabet.Ephred(e)
}
func (self *QSeq) SetE(pos seq.Position, l float64) {
self.S[pos.Pos-self.offset][pos.Ind].Q = alphabet.Ephred(l)
}
func (self *Phred) SetE(pos seq.Position, e float64) {
self.S[pos.Pos-self.offset] = alphabet.Ephred(e)
}
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)))),
}
}
// Tolerance on float comparison for QConsensify
var FloatTolerance float64 = 1e-10
// A default Consensifyer function that takes letter quality into account.
// http://staden.sourceforge.net/manual/gap4_unix_120.html
var QConsensify = func(a Aligned, pos int, fill bool) alphabet.QLetter {
alpha := a.Alphabet()
w := make([]float64, alpha.Len())
for i := range w {
w[i] = 1
}