correction of several small bugs

pkg/obialign/locatepattern.go

@@ -1,30 +1,72 @@
 package obialign
 
+import log "github.com/sirupsen/logrus"
+
+// buffIndex converts a pair of coordinates (i, j) into a linear index in a matrix
+// of size width x width. The coordinates are (-1)-indexed, and the linear index
+// is 0-indexed as well. The function first adds 1 to both coordinates to make
+// sure the (-1,-1) coordinate is at position 0 in the matrix, and then computes
+// the linear index by multiplying the first coordinate by the width and adding
+// the second coordinate.
 func buffIndex(i, j, width int) int {
 	return (i+1)*width + (j + 1)
 }
+
+// LocatePattern is a function to locate a pattern in a sequence.
+//
+// It uses a dynamic programming approach to build a matrix of scores.
+// The score at each cell is the maximum of the score of the cell
+// above it (representing a deletion), the score of the cell to its
+// left (representing an insertion), and the score of the cell
+// diagonally above it (representing a match).
+//
+// The score of a match is 0 if the two characters are the same,
+// and -1 if they are different.
+//
+// The function returns the start and end positions of the best
+// match, as well as the number of errors in the best match.
 func LocatePattern(pattern, sequence []byte) (int, int, int) {
+	// Pattern spreads over the columns
+	// Sequence spreads over the rows
 	width := len(pattern) + 1
 	buffsize := (len(pattern) + 1) * (len(sequence) + 1)
 	buffer := make([]int, buffsize)
+
+	if len(pattern) >= len(sequence) {
+		log.Panicf("Pattern %s must be shorter than sequence %s", pattern, sequence)
+	}
+
+	// The path matrix keeps track of the best path through the matrix
+	//  0 : indicate the diagonal path
+	//  1 : indicate the up path
+	// -1 : indicate the left path
 	path := make([]int, buffsize)
 
+	// Initialize the first row of the matrix
 	for j := 0; j < len(pattern); j++ {
 		idx := buffIndex(-1, j, width)
 		buffer[idx] = -j - 1
 		path[idx] = -1
 	}
 
+	// Initialize the first column of the matrix
+	// Alignment is endgap free so first column = 0
+	// to allow primer to shift freely along the sequence
 	for i := -1; i < len(sequence); i++ {
 		idx := buffIndex(i, -1, width)
 		buffer[idx] = 0
 		path[idx] = +1
 	}
 
+	// Fills the matrix except the last column
+	// where gaps must be free too.
 	path[0] = 0
 	jmax := len(pattern) - 1
 	for i := 0; i < len(sequence); i++ {
 		for j := 0; j < jmax; j++ {
+
+			// Mismatch score = -1
+			// Match score = 0
 			match := -1
 			if _samenuc(pattern[j], sequence[i]) {
 				match = 0
@@ -33,6 +75,8 @@ func LocatePattern(pattern, sequence []byte) (int, int, int) {
 			idx := buffIndex(i, j, width)
 
 			diag := buffer[buffIndex(i-1, j-1, width)] + match
+
+			// Each gap cost -1
 			left := buffer[buffIndex(i, j-1, width)] - 1
 			up := buffer[buffIndex(i-1, j, width)] - 1
 
@@ -51,9 +95,12 @@ func LocatePattern(pattern, sequence []byte) (int, int, int) {
 		}
 	}
 
+	// Fills the last column considering the free up gap
 	for i := 0; i < len(sequence); i++ {
 		idx := buffIndex(i, jmax, width)
 
+		// Mismatch score = -1
+		// Match score = 0
 		match := -1
 		if _samenuc(pattern[jmax], sequence[i]) {
 			match = 0
@@ -65,6 +112,7 @@ func LocatePattern(pattern, sequence []byte) (int, int, int) {
 
 		score := max(diag, up, left)
 		buffer[idx] = score
+
 		switch {
 		case score == left:
 			path[idx] = -1
@@ -75,11 +123,13 @@ func LocatePattern(pattern, sequence []byte) (int, int, int) {
 		}
 	}
 
+	// Bactracking of the aligment
+
 	i := len(sequence) - 1
 	j := jmax
 	end := -1
 	lali := 0
-	for i > -1 && j > 0 {
+	for j > 0 { // C'était i > -1 && j > 0
 		lali++
 		switch path[buffIndex(i, j, width)] {
 		case 0:
@@ -100,5 +150,9 @@ func LocatePattern(pattern, sequence []byte) (int, int, int) {
 		}
 
 	}
+
+	// log.Warnf("from : %d to: %d error: %d match: %v",
+	// 	i, end+1, -buffer[buffIndex(len(sequence)-1, len(pattern)-1, width)],
+	// 	string(sequence[i:(end+1)]))
 	return i, end + 1, -buffer[buffIndex(len(sequence)-1, len(pattern)-1, width)]
 }