From a0a9fb461c2d95d0b7c7e455772823c55cd2e29d Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Tue, 4 Jun 2024 16:50:07 +0200
Subject: [PATCH] trial on rewriting obimultiplex

Former-commit-id: d00f3353d83760dc878c6411ad344d96216096a7
---
 cmd/obitools/obimultiplex2/main.go | 56 ++++++++++++++++++++++++++++++
 1 file changed, 56 insertions(+)
 create mode 100644 cmd/obitools/obimultiplex2/main.go

diff --git a/cmd/obitools/obimultiplex2/main.go b/cmd/obitools/obimultiplex2/main.go
new file mode 100644
index 0000000..6edb181
--- /dev/null
+++ b/cmd/obitools/obimultiplex2/main.go
@@ -0,0 +1,56 @@
+package main
+
+import (
+	"fmt"
+	"os"
+
+	log "github.com/sirupsen/logrus"
+
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obimultiplex2"
+)
+
+func main() {
+
+	// f, err := os.Create("cpu.pprof")
+	// if err != nil {
+	// 	log.Fatal(err)
+	// }
+	// pprof.StartCPUProfile(f)
+	// defer pprof.StopCPUProfile()
+
+	// ftrace, err := os.Create("cpu.trace")
+	// if err != nil {
+	// 	log.Fatal(err)
+	// }
+	// trace.Start(ftrace)
+	// defer trace.Stop()
+
+	optionParser := obioptions.GenerateOptionParser(obimultiplex2.OptionSet)
+
+	_, args := optionParser(os.Args)
+
+	if obimultiplex2.CLIAskConfigTemplate() {
+		fmt.Print(obimultiplex2.CLIConfigTemplate())
+		os.Exit(0)
+	}
+
+	if !obimultiplex2.CLIHasNGSFilterFile() {
+		log.Error("You must provide a tag list file following the NGSFilter format")
+		os.Exit(1)
+	}
+
+	sequences, err := obiconvert.CLIReadBioSequences(args...)
+
+	if err != nil {
+		log.Errorf("Cannot open file (%v)", err)
+		os.Exit(1)
+	}
+	amplicons, _ := obimultiplex2.IExtractBarcode(sequences)
+	obiconvert.CLIWriteBioSequences(amplicons, true)
+	amplicons.Wait()
+	obiiter.WaitForLastPipe()
+
+}