From e863dc456a636a000f6e39e957963618252ed091 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Tue, 28 Mar 2023 20:07:26 +0700
Subject: [PATCH] Add an option --pprof

Former-commit-id: 3ca1280e8daddbf1075e3189f9851211ce8882ae
---
 cmd/obitools/obipcr/main.go | 14 ++++++--------
 pkg/obioptions/options.go   | 11 +++++++++++
 pkg/obiseq/pool.go          |  8 +++++++-
 3 files changed, 24 insertions(+), 9 deletions(-)

diff --git a/cmd/obitools/obipcr/main.go b/cmd/obitools/obipcr/main.go
index c256d71..d925d4f 100644
--- a/cmd/obitools/obipcr/main.go
+++ b/cmd/obitools/obipcr/main.go
@@ -2,8 +2,10 @@ package main
 
 import (
 	"os"
+
 	log "github.com/sirupsen/logrus"
 
+
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
@@ -12,13 +14,9 @@ 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 pprof -nodefraction=0 -http=:8081 http://localhost:8080/debug/pprof/allocs
+	// look at http://localhost:8080/debug/pprof for havng the possibilities
+	//go http.ListenAndServe("localhost:8080", nil)
 
 	// go tool trace cpu.trace
 	// ftrace, err := os.Create("cpu.trace")
@@ -35,7 +33,7 @@ func main() {
 	sequences, err := obiconvert.CLIReadBioSequences(args...)
 
 	if err != nil {
-		log.Errorf("Cannot open file (%v)",err)
+		log.Errorf("Cannot open file (%v)", err)
 		os.Exit(1)
 	}
 
diff --git a/pkg/obioptions/options.go b/pkg/obioptions/options.go
index 1ba683b..66077e8 100644
--- a/pkg/obioptions/options.go
+++ b/pkg/obioptions/options.go
@@ -8,12 +8,17 @@ import (
 	log "github.com/sirupsen/logrus"
 
 	"github.com/DavidGamba/go-getoptions"
+
+	"net/http"
+	_ "net/http/pprof"
+
 )
 
 var _Debug = false
 var _ParallelWorkers = runtime.NumCPU()*2 - 1
 var _MaxAllowedCPU = runtime.NumCPU()
 var _BatchSize = 5000
+var _Pprof = false
 
 type ArgumentParser func([]string) (*getoptions.GetOpt, []string)
 
@@ -24,6 +29,7 @@ func GenerateOptionParser(optionset ...func(*getoptions.GetOpt)) ArgumentParser
 	options.SetUnknownMode(getoptions.Fail)
 	options.Bool("help", false, options.Alias("h", "?"))
 	options.BoolVar(&_Debug, "debug", false)
+	options.BoolVar(&_Pprof, "pprof", false)
 
 	options.IntVar(&_ParallelWorkers, "workers", _ParallelWorkers,
 		options.Alias("w"),
@@ -52,6 +58,11 @@ func GenerateOptionParser(optionset ...func(*getoptions.GetOpt)) ArgumentParser
 			log.Debugln("Switch to debug level logging")
 		}
 
+		if options.Called("pprof") {
+			go http.ListenAndServe("localhost:8080", nil)
+			log.Infoln("Start a pprof server at address http://localhost:8080/debug/pprof")
+		}
+
 		// Handle user errors
 		if err != nil {
 			fmt.Fprintf(os.Stderr, "ERROR: %s\n\n", err)
diff --git a/pkg/obiseq/pool.go b/pkg/obiseq/pool.go
index 08d2806..0b7d1be 100644
--- a/pkg/obiseq/pool.go
+++ b/pkg/obiseq/pool.go
@@ -45,7 +45,13 @@ func GetSlice(capacity int) []byte {
 }
 
 func CopySlice(src []byte) []byte {
-	sl := GetSlice(len(src))[0:len(src)]
+	sl := GetSlice(len(src))
+
+	if cap(sl) < len(src) {
+		log.Panicln("Bizarre... j'aurai pourtant cru")
+	}
+	
+	sl = sl[0:len(src)]
 
 	copy(sl, src)