Add option related to agrep match on obigrep and obiannotate

pkg/obiapat/predicat.go

@@ -0,0 +1,40 @@
+package obiapat
+
+import (
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
+	log "github.com/sirupsen/logrus"
+)
+
+func IsPatternMatchSequence(pattern string, errormax int, bothStrand, allowIndels bool) obiseq.SequencePredicate {
+
+	pat, err := MakeApatPattern(pattern, errormax, allowIndels)
+
+	if err != nil {
+		log.Fatalf("error in sequence regular pattern syntax : %v", err)
+	}
+
+	cpat, err := pat.ReverseComplement()
+
+	if err != nil {
+		log.Fatalf("cannot reverse complement the pattern : %v", err)
+	}
+
+	f := func(sequence *obiseq.BioSequence) bool {
+		aseq, err := MakeApatSequence(sequence, false)
+
+		if err != nil {
+			log.Panicf("Cannot convert sequence %s to apat format", sequence.Id())
+		}
+
+		match := pat.IsMatching(aseq, 0, aseq.Len())
+
+		if !match && bothStrand {
+
+			match = cpat.IsMatching(aseq, 0, aseq.Len())
+		}
+
+		return match
+	}
+
+	return f
+}