From f1e3a68dc49bcce4d42fbbcb450f2d6a1e499211 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Sun, 21 Aug 2022 13:44:09 +0200
Subject: [PATCH] improved performance

---
 cmd/obitools/obipcr/main.go | 27 ++++++++++++++-------------
 pkg/obitools/obipcr/pcr.go  |  3 ++-
 2 files changed, 16 insertions(+), 14 deletions(-)

diff --git a/cmd/obitools/obipcr/main.go b/cmd/obitools/obipcr/main.go
index 5ecf59f..889eee2 100644
--- a/cmd/obitools/obipcr/main.go
+++ b/cmd/obitools/obipcr/main.go
@@ -1,9 +1,10 @@
 package main
 
 import (
-	log "github.com/sirupsen/logrus"
 	"os"
-	"runtime/trace"
+	"runtime/pprof"
+
+	log "github.com/sirupsen/logrus"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
@@ -13,20 +14,20 @@ import (
 func main() {
 
 	// go tool pprof -http=":8000" ./obipairing ./cpu.pprof
-	// f, err := os.Create("cpu.pprof")
-	// if err != nil {
-	// 	log.Fatal(err)
-	// }
-	// pprof.StartCPUProfile(f)
-	// defer pprof.StopCPUProfile()
-
-	// go tool trace cpu.trace
-	ftrace, err := os.Create("cpu.trace")
+	f, err := os.Create("cpu.pprof")
 	if err != nil {
 		log.Fatal(err)
 	}
-	trace.Start(ftrace)
-	defer trace.Stop()
+	pprof.StartCPUProfile(f)
+	defer pprof.StopCPUProfile()
+
+	// go tool trace cpu.trace
+	// ftrace, err := os.Create("cpu.trace")
+	// if err != nil {
+	// 	log.Fatal(err)
+	// }
+	// trace.Start(ftrace)
+	// defer trace.Stop()
 
 	optionParser := obioptions.GenerateOptionParser(obipcr.OptionSet)
 
diff --git a/pkg/obitools/obipcr/pcr.go b/pkg/obitools/obipcr/pcr.go
index 7515dfa..466e779 100644
--- a/pkg/obitools/obipcr/pcr.go
+++ b/pkg/obitools/obipcr/pcr.go
@@ -3,6 +3,7 @@ package obipcr
 import (
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiapat"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
 )
 
 // PCR iterates over sequences provided by a obiseq.IBioSequenceBatch
@@ -37,5 +38,5 @@ func PCR(iterator obiiter.IBioSequenceBatch) (obiiter.IBioSequenceBatch, error)
 
 	worker := obiapat.PCRSliceWorker(opts...)
 
-	return iterator.MakeISliceWorker(worker), nil
+	return iterator.MakeISliceWorker(worker, obioptions.CLIParallelWorkers(), 0), nil
 }