From a36e830de354a67186e5d406cdd054cf0cfbd1c8 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Wed, 20 Dec 2023 08:14:07 +0100
Subject: [PATCH] homogenize worker count

Former-commit-id: 4352ac6694c08023cdf0e090723fac8af655cea4
---
 pkg/obiapat/pcr.go                 | 3 ++-
 pkg/obichunk/options.go            | 6 ++++--
 pkg/obingslibrary/worker.go        | 5 +++--
 pkg/obitools/obipairing/pairing.go | 2 +-
 4 files changed, 10 insertions(+), 6 deletions(-)

diff --git a/pkg/obiapat/pcr.go b/pkg/obiapat/pcr.go
index 0a9475c..c75c307 100644
--- a/pkg/obiapat/pcr.go
+++ b/pkg/obiapat/pcr.go
@@ -3,6 +3,7 @@ package obiapat
 import (
 	log "github.com/sirupsen/logrus"
 
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )
@@ -103,7 +104,7 @@ func MakeOptions(setters []WithOption) Options {
 		extension:       -1,
 		fullExtension:   false,
 		circular:        false,
-		parallelWorkers: 4,
+		parallelWorkers: obioptions.CLIParallelWorkers(),
 		batchSize:       100,
 		forward:         NilApatPattern,
 		cfwd:            NilApatPattern,
diff --git a/pkg/obichunk/options.go b/pkg/obichunk/options.go
index d6ffa03..4d6a90d 100644
--- a/pkg/obichunk/options.go
+++ b/pkg/obichunk/options.go
@@ -1,5 +1,7 @@
 package obichunk
 
+import "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
+
 type __options__ struct {
 	statsOn         []string
 	categories      []string
@@ -24,8 +26,8 @@ func MakeOptions(setters []WithOption) Options {
 		navalue:         "NA",
 		cacheOnDisk:     false,
 		batchCount:      100,
-		batchSize:       5000,
-		parallelWorkers: 4,
+		batchSize:       obioptions.CLIBatchSize(),
+		parallelWorkers: obioptions.CLIParallelWorkers(),
 		noSingleton:     false,
 	}
 
diff --git a/pkg/obingslibrary/worker.go b/pkg/obingslibrary/worker.go
index 197407d..60909aa 100644
--- a/pkg/obingslibrary/worker.go
+++ b/pkg/obingslibrary/worker.go
@@ -1,6 +1,7 @@
 package obingslibrary
 
 import (
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 )
 
@@ -125,8 +126,8 @@ func MakeOptions(setters []WithOption) Options {
 		allowedMismatch: 0,
 		allowsIndel:     false,
 		withProgressBar: false,
-		parallelWorkers: 4,
-		batchSize:       1000,
+		parallelWorkers: obioptions.CLIParallelWorkers(),
+		batchSize:       obioptions.CLIBatchSize(),
 	}
 
 	opt := Options{&o}
diff --git a/pkg/obitools/obipairing/pairing.go b/pkg/obitools/obipairing/pairing.go
index 8589e20..42bf653 100644
--- a/pkg/obitools/obipairing/pairing.go
+++ b/pkg/obitools/obipairing/pairing.go
@@ -221,7 +221,7 @@ func IAssemblePESequencesBatch(iterator obiiter.IBioSequence,
 		log.Fatalln("Sequence data must be paired")
 	}
 
-	nworkers := obioptions.CLIMaxCPU() * 3 / 2
+	nworkers := obioptions.CLIParallelWorkers()
 
 	if len(sizes) > 0 {
 		nworkers = sizes[0]