func findOverlaps(i int, r runner.Runner, reads []read) ([]readPair, error) {
step := int(len(reads) / r.NumRoutines())
start := step * i
end := start + step
if end > len(reads) {
end = len(reads)
}
var ret []readPair
for i := start; i < end; i++ {
tR := &reads[i]
minLen := 40
minLenRead := -1
for j, pR := range reads {
if i == j {
continue
}
lenOverlap := suffixPrefixMatch(tR.Seq, pR.Seq, minLen)
if lenOverlap > minLen {
minLen = lenOverlap
minLenRead = j
} else if lenOverlap == minLen {
minLenRead = -1
}
}
if minLenRead != -1 {
ret = append(ret, readPair{
Left: tR, Right: &reads[minLenRead], Overlap: minLen,
})
}
// maxLen := 40
// var maxRead *read
// matches, exists := prefixMap[tR.Seq[len(tR.Seq)-40:]]
// if !exists {
// continue
// }
// for j := range matches {
// pR := &reads[j]
// if tR.Label == pR.Label {
// continue
// }
// lenO := suffixPrefixMatch(tR.Seq, pR.Seq, maxLen)
// if lenO > maxLen {
// maxLen = lenO
// maxRead = pR
// } else if lenO == maxLen {
// maxRead = nil
// }
// }
// if maxRead != nil {
// ret = append(ret, readPair{
// Left: tR, Right: maxRead, Overlap: maxLen,
// })
// }
}
return ret, nil
}
func computeMatrix(i int, r runner.Runner, unitigs []*fullUnitig) ([][]int, error) {
step := int(len(unitigs) / r.NumRoutines())
start := step * i
end := start + step
if end > len(unitigs) {
end = len(unitigs)
}
results := make([][]int, end-start)
for i := range results {
results[i] = make([]int, len(unitigs))
}
for i := start; i < end; i++ {
for j := range unitigs {
if i == j {
results[i-start][j] = -1
continue
}
results[i-start][j] = suffixPrefixMatch(unitigs[i].Seq, unitigs[j].Seq, 0)
}
}
return results, nil
}