Small change in parallelisation tuning

Former-commit-id: 3fe2495b7fd86a0ba47dd87907323a457bae481a

cmd/obitools/obipcr/main.go

@@ -25,7 +25,8 @@ func main() {
 	// trace.Start(ftrace)
 	// defer trace.Stop()
 
-	obioptions.SetWorkerPerCore(1)
+	obioptions.SetWorkerPerCore(2)
+	obioptions.SetReadWorkerPerCore(0.5)
 
 	optionParser := obioptions.GenerateOptionParser(obipcr.OptionSet)
 

pkg/obioptions/options.go

@@ -14,7 +14,8 @@ import (
 )
 
 var _Debug = false
-var _WorkerPerCore = 2
+var _WorkerPerCore = 2.0
+var _ReadWorkerPerCore = 1.0
 var _MaxAllowedCPU = runtime.NumCPU()
 var _BatchSize = 5000
 var _Pprof = false
@@ -92,9 +93,14 @@ func CLIIsDebugMode() bool {
 // CLIParallelWorkers returns the number of parallel workers requested by
 // the command line option --workers|-w.
 func CLIParallelWorkers() int {
-	return _MaxAllowedCPU * _WorkerPerCore
+	return int(float64(_MaxAllowedCPU) * float64(_WorkerPerCore))
 }
 
+func CLIReadParallelWorkers() int {
+	return int(float64(_MaxAllowedCPU) * float64(_ReadWorkerPerCore))
+}
+
+
 // CLIParallelWorkers returns the number of parallel workers requested by
 // the command line option --workers|-w.
 func CLIMaxCPU() int {
@@ -116,14 +122,22 @@ func DebugOff() {
 	_Debug = false
 }
 
-func SetWorkerPerCore(n int) {
+func SetWorkerPerCore(n float64) {
 	_WorkerPerCore = n
 }
 
-func WorkerPerCore() int {
+func SetReadWorkerPerCore(n float64) {
+	_ReadWorkerPerCore = n
+}
+
+func WorkerPerCore() float64 {
 	return _WorkerPerCore
 }
 
+func ReadWorkerPerCore() float64 {
+	return _ReadWorkerPerCore
+}
+
 func SetBatchSize(n int) {
 	_BatchSize = n
 }

pkg/obitools/obiconvert/sequence_reader.go

@@ -90,7 +90,7 @@ func CLIReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
 		opts = append(opts, obiformats.OptionsFastSeqHeaderParser(obiformats.ParseGuessedFastSeqHeader))
 	}
 
-	nworkers := obioptions.CLIParallelWorkers()
+	nworkers := obioptions.CLIReadParallelWorkers()
 	if nworkers < 2 {
 		nworkers = 2
 	}

pkg/obitools/obimultiplex/demultiplex.go

@@ -56,5 +56,5 @@ func IExtractBarcode(iterator obiiter.IBioSequence) (obiiter.IBioSequence, error
 	}
 	log.Printf("Sequence demultiplexing using %d workers\n", obioptions.CLIParallelWorkers())
 
-	return newIter.Speed("Demultiplexing"), nil
+	return newIter, nil
 }

pkg/obitools/obitag/obitag.go

@@ -1,11 +1,12 @@
 package obitag
 
 import (
-	"log"
 	"math"
 	"strconv"
 	"strings"
 
+	log "github.com/sirupsen/logrus"
+
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obialign"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obikmer"