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Add obiminion first version

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Former-commit-id: aa5ace7bd4d2266333715fca7094d1c3cbbb5e6d
This commit is contained in:
Eric Coissac
2024-05-14 08:16:12 +02:00
parent 9e63013bc2
commit 017030bcce
24 changed files with 1599 additions and 469 deletions
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41
pkg/obialign/fastlcsegf.go
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@@ -130,11 +130,11 @@ func FastLCSEGFScoreByte(bA, bB []byte, maxError int, endgapfree bool, buffer *[
// in_matrix := false
x1 := y - lB + extra
x2 := extra - y
xs := obiutils.MaxInt(obiutils.MaxInt(x1, x2), 0)
xs := obiutils.Max(obiutils.Max(x1, x2), 0)
x1 = y + extra
x2 = lA + extra - y
xf := obiutils.MinInt(obiutils.MinInt(x1, x2), even-1) + 1
xf := obiutils.Min(obiutils.Min(x1, x2), even-1) + 1
for x := xs; x < xf; x++ {
@@ -222,11 +222,11 @@ func FastLCSEGFScoreByte(bA, bB []byte, maxError int, endgapfree bool, buffer *[
// . 9 10 + 2 - 1
x1 = y - lB + extra + even
x2 = extra - y + even - 1
xs = obiutils.MaxInt(obiutils.MaxInt(x1, x2), even)
xs = obiutils.Max(obiutils.Max(x1, x2), even)
x1 = y + extra + even
x2 = lA + extra - y + even - 1
xf = obiutils.MinInt(obiutils.MinInt(x1, x2), width-1) + 1
xf = obiutils.Min(obiutils.Min(x1, x2), width-1) + 1
for x := xs; x < xf; x++ {
@@ -348,16 +348,15 @@ func FastLCSEGFScoreByte(bA, bB []byte, maxError int, endgapfree bool, buffer *[
// - Matching: 1
// - Mismatch or gap: 0
//
// Compared to FastLCSScoreByte the length of the shortest alignment returned does not include the end-gaps.
// Parameters:
// - seqA: The first bio sequence.
// - seqB: The second bio sequence.
// - maxError: The maximum allowed error between the sequences. If set to -1, no limit is applied.
// - buffer: A pointer to a uint64 slice to store intermediate results. If nil, a new slice is created.
//
// if buffer != nil, the buffer is used to store intermediate results.
// Otherwise, a new buffer is allocated.
//
// seqA: The first bio sequence.
// seqB: The second bio sequence.
// maxError: The maximum allowed error between the sequences.
// buffer: A buffer to store intermediate results.
// Returns the score of the longest common subsequence and the length of the shortest alignment corresponding.
// Returns:
// - The score of the longest common subsequence.
// - The length of the shortest alignment corresponding to the LCS.
func FastLCSEGFScore(seqA, seqB *obiseq.BioSequence, maxError int, buffer *[]uint64) (int, int) {
return FastLCSEGFScoreByte(seqA.Sequence(), seqB.Sequence(), maxError, true, buffer)
}
@@ -372,14 +371,16 @@ func FastLCSEGFScore(seqA, seqB *obiseq.BioSequence, maxError int, buffer *[]uin
// - Matching: 1
// - Mismatch or gap: 0
//
// if buffer != nil, the buffer is used to store intermediate results.
// Otherwise, a new buffer is allocated.
// Parameters:
// - seqA: The first bio sequence.
// - seqB: The second bio sequence.
// - maxError: The maximum allowed error between the sequences. If set to -1, no limit is applied.
// - buffer: A pointer to a uint64 slice to store intermediate results. If nil, a new slice is created.
//
// seqA: The first bio sequence.
// seqB: The second bio sequence.
// maxError: The maximum allowed error between the sequences.
// buffer: A buffer to store intermediate results.
// Returns the score of the longest common subsequence and the length of the shortest alignment corresponding.
// Returns:
// - The score of the longest common subsequence.
// - The length of the shortest alignment corresponding to the LCS.
func FastLCSScore(seqA, seqB *obiseq.BioSequence, maxError int, buffer *[]uint64) (int, int) {
return FastLCSEGFScoreByte(seqA.Sequence(), seqB.Sequence(), maxError, false, buffer)
}