Several bug in annotation management

pkg/obiseq/revcomp.go

@@ -1,7 +1,7 @@
 package obiseq
 
 // ".ABCDEFGHIJKLMNOPQRSTUVWXYZ#![]"
-var __revcmp_dna__ = []byte(".TVGHEFCDIJMLKNOPQYSAABWXRZ#!][")
+var _revcmpDNA = []byte(".TVGHEFCDIJMLKNOPQYSAABWXRZ#!][")
 
 // Reverse complements a DNA sequence.
 // If the inplace parametter is true, that operation is done in place.
@@ -15,8 +15,11 @@ func (sequence *BioSequence) ReverseComplement(inplace bool) *BioSequence {
 
 	for i, j := sequence.Length()-1, 0; i >= j; i-- {
 
-		s[j], s[i] = __revcmp_dna__[s[i]&31]|(s[i]&0x20),
-			__revcmp_dna__[s[j]&31]|(s[j]&0x20)
+		// ASCII code & 31 -> builds an index in witch (a|A) is 1
+		// ASCII code & 0x20 -> Foce lower case
+
+		s[j], s[i] = _revcmpDNA[s[i]&31]|(s[i]&0x20),
+			_revcmpDNA[s[j]&31]|(s[j]&0x20)
 		j++
 	}
 
@@ -28,5 +31,36 @@ func (sequence *BioSequence) ReverseComplement(inplace bool) *BioSequence {
 		}
 	}
 
+	return sequence._revcmpMutation()
+}
+
+func (sequence *BioSequence) _revcmpMutation() *BioSequence {
+
+	rev := func(m string) string {
+		b := []byte(m)
+
+		// Echange and reverse complement symboles
+		b[1], b[9] = _revcmpDNA[b[9]&31]|(b[9]&0x20),
+			_revcmpDNA[b[1]&31]|(b[1]&0x20)
+
+		// Exchange sequencing scores
+		b[3], b[4], b[11], b[12] = b[11], b[12], b[3], b[4]
+
+		return string(b)
+	}
+
+	lseq := sequence.Length()
+
+	mut, ok := sequence.GetIntMap("pairing_mismatches")
+	if ok && len(mut) > 0 {
+		cmut := make(map[string]int, len(mut))
+
+		for m, p := range mut {
+			cmut[rev(m)] = lseq - p + 1
+		}
+
+		sequence.SetAttribute("pairing_mismatches", cmut)
+	}
+
 	return sequence
 }