Adds a JSON output format

Former-commit-id: 26f07460772c0f735bf705d473f892878d3e57f0

pkg/obiformats/fastqseq_write_generic.go

@@ -0,0 +1,47 @@
+package obiformats
+
+import (
+	"bytes"
+
+	log "github.com/sirupsen/logrus"
+
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
+)
+
+type BioSequenceBatchFormater func(batch obiiter.BioSequenceBatch) []byte
+type BioSequenceFormater func(sequence *obiseq.BioSequence) string
+
+func BuildFastxSeqFormater(format string, header FormatHeader) BioSequenceFormater {
+	var f BioSequenceFormater
+
+	switch format {
+	case "fastq":
+		f = func(sequence *obiseq.BioSequence) string {
+			return FormatFastq(sequence, header)
+		}
+	case "fasta":
+		f = func(sequence *obiseq.BioSequence) string {
+			return FormatFasta(sequence, header)
+		}
+	default:
+		log.Fatal("Unknown output format")
+	}
+
+	return f
+}
+
+func BuildFastxFormater(format string, header FormatHeader) BioSequenceBatchFormater {
+	fs := BuildFastxSeqFormater(format, header)
+
+	f := func(batch obiiter.BioSequenceBatch) []byte {
+		var bs bytes.Buffer
+		for _, seq := range batch.Slice() {
+			bs.WriteString(fs(seq))
+			bs.WriteString("\n")
+		}
+		return bs.Bytes()
+	}
+
+	return f
+}