Several bug in annotation management

pkg/obiseq/biosequence.go

@@ -257,6 +257,20 @@ func (s *BioSequence) GetBool(key string) (bool, bool) {
 	return val, ok
 }
 
+func (s *BioSequence) GetIntMap(key string) (map[string]int, bool) {
+	var val map[string]int
+	var err error
+
+	v, ok := s.GetAttribute(key)
+
+	if ok {
+		val, err = goutils.InterfaceToIntMap(v)
+		ok = err == nil
+	}
+
+	return val, ok
+}
+
 // Returning the MD5 hash of the sequence.
 func (s *BioSequence) MD5() [16]byte {
 	return md5.Sum(s.sequence)

pkg/obiseq/pool.go

@@ -41,7 +41,7 @@ func GetSlice(capacity int) []byte {
 
 func CopySlice(src []byte) []byte {
 	sl := GetSlice(len(src))
-	copy(sl,src)
+	copy(sl, src)
 	return sl
 }
 
@@ -69,7 +69,7 @@ func GetAnnotation(values ...Annotation) Annotation {
 	}
 
 	if len(values) > 0 {
-		goutils.CopyMap(a, values[0])
+		goutils.MustFillMap(a, values[0])
 	}
 
 	return a

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
 }

pkg/obiseq/subseq.go

@@ -43,9 +43,30 @@ func (sequence *BioSequence) Subsequence(from, to int, circular bool) (*BioSeque
 
 	}
 
-	if len(sequence.Annotations()) > 0 {
+	if sequence.HasAnnotation() {
 		newSeq.annotations = GetAnnotation(sequence.Annotations())
 	}
 
-	return newSeq, nil
+	return newSeq._subseqMutation(from), nil
+}
+
+func (sequence *BioSequence) _subseqMutation(shift int) *BioSequence {
+
+	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 {
+			if p < lseq {
+				cmut[m] = p - shift
+			}
+		}
+
+		sequence.SetAttribute("pairing_mismatches", cmut)
+	}
+
+	return sequence
+
 }