Patch a bug in Subsequence and adds few unit tests.

Former-commit-id: caddc9ad6523e4ef02899bfe83cc8681ef674383

pkg/obiseq/revcomp.go

@@ -3,18 +3,44 @@ package obiseq
 // ".ABCDEFGHIJKLMNOPQRSTUVWXYZ#![]"
 var _revcmpDNA = []byte(".TVGHNNCDNNMNKNNNNYSAABWNRN]N[NNN")
 
-func complement(n byte) byte {
+// nucComplement returns the complement of a nucleotide.
+//
+// It takes a byte as input and returns the complement of the nucleotide.
+// The function handles various cases:
+//   - If the input is '.' or '-', it returns the same character.
+//   - If the input is '[', it returns ']'.
+//   - If the input is ']', it returns '['.
+//   - If the input is a letter from 'A' to 'z', it returns the complement of the nucleotide.
+//     The complement is calculated using the _revcmpDNA lookup table.
+//   - If none of the above cases match, it returns 'n'.
+func nucComplement(n byte) byte {
 	switch {
 	case n == '.' || n == '-':
 		return n
+	case n == '[':
+		return ']'
+	case n == ']':
+		return '['
 	case (n >= 'A' && n <= 'z'):
-		return _revcmpDNA[n&31] | (n & 0x20)
+		return _revcmpDNA[n&31] | 0x20
 	}
 	return 'n'
 }
 
-// Reverse complements a DNA sequence.
-// If the inplace parametter is true, that operation is done in place.
+// ReverseComplement reverses and complements a BioSequence.
+//
+// If `inplace` is `false`, a new copy of the BioSequence is created before
+// performing the reverse complement. If `inplace` is `true`, the reverse
+// complement is performed directly on the original BioSequence.
+//
+// The function first reverses the sequence by swapping the characters from the
+// beginning and end of the sequence. Then, it complements each character in the
+// sequence by finding its complement using the `nucComplement` function.
+//
+// If the BioSequence has qualities, the function also reverse the qualities in
+// the same way as the sequence.
+//
+// The function returns the reverse complemented BioSequence.
 func (sequence *BioSequence) ReverseComplement(inplace bool) *BioSequence {
 
 	if !inplace {
@@ -28,7 +54,7 @@ func (sequence *BioSequence) ReverseComplement(inplace bool) *BioSequence {
 		// ASCII code & 31 -> builds an index in witch (a|A) is 1
 		// ASCII code & 0x20 -> Foce lower case
 
-		s[j], s[i] = complement(s[i]), complement(s[j])
+		s[j], s[i] = nucComplement(s[i]), nucComplement(s[j])
 		j++
 	}
 
@@ -49,7 +75,7 @@ func (sequence *BioSequence) _revcmpMutation() *BioSequence {
 		b := []byte(m)
 
 		// Echange and reverse complement symboles
-		b[1], b[9] = complement(b[9]), complement(b[1])
+		b[1], b[9] = nucComplement(b[9]), nucComplement(b[1])
 
 		// Exchange sequencing scores
 		b[3], b[4], b[11], b[12] = b[11], b[12], b[3], b[4]