A first functional version of obiclean

pkg/obialign/is_d0_or_d1.go

@@ -0,0 +1,78 @@
+package obialign
+
+import "git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
+
+func abs(x int) int {
+	if x < 0 {
+		return -x
+	}
+
+	return x
+}
+
+func D1Or0(seq1, seq2 *obiseq.BioSequence) (int, int, byte, byte) {
+
+	pos := -1
+
+	l1 := seq1.Length()
+	l2 := seq2.Length()
+
+	if abs(l1-l2) > 1 {
+		return -1, pos, 0, 0
+	}
+
+	s1 := seq1.Sequence()
+	s2 := seq2.Sequence()
+
+	b1 := 0
+	b2 := 0
+
+	// Scans the sequences from their beginings as long as they are identical
+
+	for b1 < l1 && b2 < l2 && s1[b1] == s2[b2] {
+		b1++
+		b2++
+	}
+
+	if b1 == l1 && b2 == l2 {
+		return 0, pos, 0, 0
+	}
+
+	// Scans the sequences from their ends as long as they are identical
+
+	e1 := l1 - 1
+	e2 := l2 - 1
+
+	for (e1 > b1 || e2 > b2) && s1[e1] == s2[e2] {
+		e1--
+		e2--
+	}
+
+	if (l1 == l2 && (e1 > b1 || e2 > b2)) ||
+		(l1 > l2 && e1 > b1) ||
+		(l1 < l2 && e2 > b2) {
+		return -1, pos, 0, 0
+	}
+
+	if b1 >= e1 {
+		if e1 > e2 {
+			pos = e1
+		} else {
+			pos = e2
+		}
+	}
+
+	a1 := byte('-')
+	a2 := byte('-')
+
+	if e2 >= e1 {
+		a2 = s2[e2]
+	}
+
+	if e2 <= e1 {
+		a1 = s1[e1]
+	}
+
+	return 1, pos, a1, a2
+
+}