func main() {
g_normalize_flag = true
if len(os.Args) < 3 {
fmt.Fprintf(os.Stderr, "provide filenames\n")
os.Exit(1)
}
fn0 := os.Args[1]
fn1 := os.Args[2]
s0, e := ioutil.ReadFile(fn0)
if e != nil {
panic(e)
}
s1, e := ioutil.ReadFile(fn1)
if e != nil {
panic(e)
}
for i := 0; i < 256; i++ {
memz.Score['n'][i] = 0
memz.Score[i]['n'] = 0
}
X, Y, sc := memz.Hirschberg(s0, s1)
if g_normalize_flag {
memz.SeqPairNormalize(X, Y)
}
//memz.Simp_b(s0,s1,0,0)
fmt.Printf("%d\n%s\n%s\n", sc, X, Y)
}
func (g *FastJInfo) EmitAlignedInterleave(ref, alt0, alt1 []byte, out *bufio.Writer) {
length_bound := 10000
if len(ref) == 0 {
return
}
p0 := make([]byte, 0, len(ref))
p1 := make([]byte, 0, len(ref))
// We can bypass doing a string alignment if they're equal, so test
// for equal (considering 'n' (nocall) entries as wildcards).
//
if !_noc_eq(ref, alt0) {
if (len(ref) > length_bound) || (len(alt0) > length_bound) {
ref0, algn0 := g.ClumsyAlign(ref, alt0)
for ii := 0; ii < len(ref0); ii++ {
p0 = append(p0, pasta.SubMap[ref0[ii]][algn0[ii]])
}
} else {
ref0, algn0, sc0 := memz.Hirschberg(ref, alt0)
_ = sc0
for ii := 0; ii < len(ref0); ii++ {
p0 = append(p0, pasta.SubMap[ref0[ii]][algn0[ii]])
}
}
} else {
for ii := 0; ii < len(ref); ii++ {
p0 = append(p0, pasta.SubMap[ref[ii]][alt0[ii]])
}
}
if !_noc_eq(ref, alt1) {
if (len(ref) > length_bound) || (len(alt1) > length_bound) {
ref1, algn1 := g.ClumsyAlign(ref, alt1)
for ii := 0; ii < len(ref1); ii++ {
p1 = append(p1, pasta.SubMap[ref1[ii]][algn1[ii]])
}
} else {
ref1, algn1, sc1 := memz.Hirschberg(ref, alt1)
_ = sc1
for ii := 0; ii < len(ref1); ii++ {
p1 = append(p1, pasta.SubMap[ref1[ii]][algn1[ii]])
}
}
} else {
for ii := 0; ii < len(ref); ii++ {
p1 = append(p1, pasta.SubMap[ref[ii]][alt1[ii]])
}
}
r0 := bytes.NewReader(p0)
r1 := bytes.NewReader(p1)
g.Out = out
pasta.InterleaveStreams(r0, r1, g)
}