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qscore.go
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qscore.go
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// Copyright ©2011-2012 Dan Kortschak <dan.kortschak@adelaide.edu.au>
//
// This program is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// (at your option) any later version.
//
// This program is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with this program. If not, see <http://www.gnu.org/licenses/>.
package seq
import (
"math"
)
type Encoding byte
const (
Sanger Encoding = iota
Solexa
Illumina1_3
Illumina1_5
Illumina1_8
)
type Qscore interface {
Encode(Encoding) byte
ProbE() float64
}
type Qsanger int8
func (self Qsanger) ToSolexa() Qsolexa {
return Qsolexa(10 * math.Log10(math.Pow(10, float64(self)/10)-1))
}
func (self Qsanger) Encode(encoding Encoding) (q byte) {
switch encoding {
case Sanger, Illumina1_8:
q = byte(self)
if q <= 93 {
q += 33
}
case Illumina1_3:
q = byte(self)
if q <= 62 {
q += 64
}
case Illumina1_5:
q = byte(self)
if q <= 62 {
q += 64
}
if q < 'B' {
q = 'B'
}
case Solexa:
q = byte(self.ToSolexa())
if q <= 62 {
q += 64
}
}
return q
}
func (self Qsanger) ProbE() float64 {
return math.Pow(10, -(float64(self) / 10))
}
type Qsolexa int8
func (self Qsolexa) ToSanger() Qsanger {
return Qsanger(10 * math.Log10(math.Pow(10, float64(self)/10)+1))
}
func (self Qsolexa) Encode(encoding Encoding) (q byte) {
switch encoding {
case Sanger, Illumina1_8:
q = byte(self.ToSanger())
if q <= 93 {
q += 33
}
case Illumina1_3:
q = byte(self.ToSanger())
if q <= 62 {
q += 64
}
case Illumina1_5:
q = byte(self.ToSanger())
if q <= 62 {
q += 64
}
if q < 'B' {
q = 'B'
}
case Solexa:
q = byte(self)
if q <= 62 {
q += 64
}
}
return q
}
func (self Qsolexa) ProbE() float64 {
pq := math.Pow(10, -(float64(self) / 10))
return pq / (1 + pq)
}