obitools/obitools4
2
0
Fork 0
mirror of https://github.com/metabarcoding/obitools4.git synced 2025-12-08 16:50:27 +00:00
Code Issues Packages Projects Releases Wiki Activity

Add some doc and switch to the parallel gzip library

Browse Source 
Former-commit-id: 2c1187001f989ba3de5895f516d4c8b54d52a4c4
This commit is contained in:
Eric Coissac
2023-08-25 14:36:38 +02:00
parent 8a98210103
commit 2a11adb346
8 changed files with 233 additions and 5 deletions
Download Patch File Download Diff File Expand all files Collapse all files

60
pkg/obialign/fastlcsegf.go
View File

@@ -31,6 +31,28 @@ func _samenuc(a, b byte) bool {
}
return a == b
}
// FastLCSEGFScoreByte calculates the score of the Longest Common Subsequence (LCS) between two byte slices.
//
// The score is calculated using the following scoring matrix:
// - Match : +1
// - Mismatch and gap: 0
//
// The LCS is calculated using the Needleman-Wunsch algorithm.
// At the same time the length of the shortest path between the two sequences is calculated.
// If the endgapfree flag is set to true, the returned length does not include the end gaps.
// If the number of mismatches or gaps is larger than the maximum allowed error, -1 is returned for both.
//
// Parameters:
// - bA: The first byte slice.
// - bB: The second byte slice.
// - maxError: The maximum allowed error. If set to -1, no limit is applied.
// - endgapfree: A boolean flag indicating whether the LCS should be end-gap free.
// - buffer: A pointer to a uint64 slice to store intermediate results. If nil, a new slice is created.
//
// Returns:
// - The score of the LCS.
// - The length of the LCS.
func FastLCSEGFScoreByte(bA, bB []byte, maxError int, endgapfree bool, buffer *[]uint64) (int, int) {
lA := len(bA)
@@ -316,10 +338,48 @@ func FastLCSEGFScoreByte(bA, bB []byte, maxError int, endgapfree bool, buffer *[
return s, l
}
// FastLCSEGFScore calculates the score of the longest common subsequence between two bio sequences in end-gap-free mode.
//
// if maxError > 0, the maximum allowed error between the sequences is maxError.
// Otherwise, no error checking is done.
// If the actual number of errors is larger than maxError, -1 is returned for both values.
//
// The score matrix is:
// - Matching: 1
// - Mismatch or gap: 0
//
// Compared to FastLCSScoreByte the length of the shortest alignment returned does not include the end-gaps.
//
// 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.
func FastLCSEGFScore(seqA, seqB *obiseq.BioSequence, maxError int, buffer *[]uint64) (int, int) {
return FastLCSEGFScoreByte(seqA.Sequence(), seqB.Sequence(), maxError, true, buffer)
}
// FastLCSScore calculates the score of the longest common subsequence between two bio sequences.
//
// if maxError > 0, the maximum allowed error between the sequences is maxError.
// Otherwise, no error checking is done.
// If the actual number of errors is larger than maxError, -1 is returned for both values.
//
// The score matrix is:
// - Matching: 1
// - Mismatch or gap: 0
//
// 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.
func FastLCSScore(seqA, seqB *obiseq.BioSequence, maxError int, buffer *[]uint64) (int, int) {
return FastLCSEGFScoreByte(seqA.Sequence(), seqB.Sequence(), maxError, false, buffer)
}