From bc1d7b26a9f8c76aa2ff97b7bfee8352a3f65eb9 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Tue, 1 Feb 2022 18:04:11 +0100
Subject: [PATCH] adds missing file

---
 pkg/obitools/obimultiplex/demultiplex.go | 40 ++++++++++++++++++++++++
 1 file changed, 40 insertions(+)
 create mode 100644 pkg/obitools/obimultiplex/demultiplex.go

diff --git a/pkg/obitools/obimultiplex/demultiplex.go b/pkg/obitools/obimultiplex/demultiplex.go
new file mode 100644
index 0000000..1de9802
--- /dev/null
+++ b/pkg/obitools/obimultiplex/demultiplex.go
@@ -0,0 +1,40 @@
+package obimultiplex
+
+import (
+	"log"
+
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obingslibrary"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
+)
+
+func IExtractBarcodeBatches(iterator obiseq.IBioSequenceBatch) (obiseq.IBioSequenceBatch, error) {
+
+	opts := make([]obingslibrary.WithOption, 0, 10)
+
+	opts = append(opts,
+		obingslibrary.OptionAllowedMismatches(CLIAllowedMismatch()),
+		obingslibrary.OptionUnidentified(CLIUnidentifiedFileName()),
+		obingslibrary.OptionDiscardErrors(!CLIConservedErrors()),
+		obingslibrary.OptionParallelWorkers(obioptions.CLIParallelWorkers()),
+		obingslibrary.OptionBatchSize(obioptions.CLIBatchSize()),
+		obingslibrary.OptionBufferSize(obioptions.CLIBufferSize()),
+	)
+
+	ngsfilter, err := CLINGSFIlter()
+	if err != nil {
+		log.Fatalf("%v", err)
+	}
+
+	worker := obingslibrary.ExtractBarcodeSliceWorker(ngsfilter, opts...)
+
+	newIter := iterator.MakeISliceWorker(worker)
+
+	if !CLIConservedErrors() {
+		newIter = newIter.Rebatch(obioptions.CLIBatchSize())
+	}
+
+	log.Printf("Sequence demultiplexing using %d workers\n", obioptions.CLIParallelWorkers())
+
+	return newIter, nil
+}