Update of obipcr and homogenization of logging

Former-commit-id: 46abf47c19ace5248042c02cf1f81d9f6c12eb10

pkg/obitools/obiconvert/sequence_reader.go

@@ -136,7 +136,7 @@ func CLIReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
 			nreader := 1
 
 			if CLINoInputOrder() {
-				nreader = obioptions.CLIParallelWorkers()
+				nreader = obioptions.ParallelFilesRead()
 			}
 
 			iterator = obiformats.ReadSequencesBatchFromFiles(

pkg/obitools/obicsv/obicsv.go

@@ -1,7 +1,7 @@
 package obicsv
 
 import (
-	"log"
+	log "github.com/sirupsen/logrus"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiformats"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"

pkg/obitools/obigrep/grep.go

@@ -1,7 +1,7 @@
 package obigrep
 
 import (
-	"log"
+	log "github.com/sirupsen/logrus"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"

pkg/obitools/obipcr/pcr.go

@@ -60,5 +60,5 @@ func CLIPCR(iterator obiiter.IBioSequence) (obiiter.IBioSequence, error) {
 		iterator = iterator.Pipe(frags)
 	}
 
-	return iterator.MakeISliceWorker(worker, false, obioptions.CLIParallelWorkers()), nil
+	return iterator.LimitMemory(0.5).MakeISliceWorker(worker, false, obioptions.CLIParallelWorkers()), nil
 }

pkg/obitools/obirefidx/geomindexing.go

@@ -2,7 +2,7 @@ package obirefidx
 
 import (
 	"fmt"
-	"log"
+	log "github.com/sirupsen/logrus"
 	"sort"
 	"sync"
 

pkg/obitools/obirefidx/obirefidx.go

@@ -221,5 +221,5 @@ func IndexReferenceDB(iterator obiiter.IBioSequence) obiiter.IBioSequence {
 		go f()
 	}
 
-	return indexed.Rebatch(1000)
+	return indexed.Rebatch(obioptions.CLIBatchSize())
 }

pkg/obitools/obiscript/options.go

@@ -1,7 +1,8 @@
 package obiscript
 
 import (
-	"log"
+	log "github.com/sirupsen/logrus"
+
 	"os"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"

pkg/obitools/obisplit/options.go

@@ -3,7 +3,7 @@ package obisplit
 import (
 	"encoding/csv"
 	"fmt"
-	"log"
+	log "github.com/sirupsen/logrus"
 	"os"
 	"slices"
 

pkg/obitools/obitag/options.go

@@ -1,7 +1,7 @@
 package obitag
 
 import (
-	"log"
+	log "github.com/sirupsen/logrus"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiformats"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"