Adds a first version of a new obidistribute command

pkg/obitools/obidistribute/distribute.go

@@ -0,0 +1,57 @@
+package obidistribute
+
+import (
+	"log"
+
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiformats"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
+)
+
+func DistributeSequence(sequences obiseq.IBioSequenceBatch) {
+
+	opts := make([]obiformats.WithOption, 0, 10)
+
+	switch obiconvert.OutputFastHeaderFormat() {
+	case "json":
+		log.Println("On output use JSON headers")
+		opts = append(opts, obiformats.OptionsFastSeqHeaderFormat(obiformats.FormatFastSeqJsonHeader))
+	case "obi":
+		log.Println("On output use OBI headers")
+		opts = append(opts, obiformats.OptionsFastSeqHeaderFormat(obiformats.FormatFastSeqOBIHeader))
+	default:
+		log.Println("On output use JSON headers")
+		opts = append(opts, obiformats.OptionsFastSeqHeaderFormat(obiformats.FormatFastSeqJsonHeader))
+	}
+
+	nworkers := obioptions.CLIParallelWorkers() / 4
+	if nworkers < 2 {
+		nworkers = 2
+	}
+
+	opts = append(opts, obiformats.OptionsParallelWorkers(nworkers))
+	opts = append(opts, obiformats.OptionsBufferSize(obioptions.CLIBufferSize()))
+	opts = append(opts, obiformats.OptionsBatchSize(obioptions.CLIBatchSize()))
+
+	opts = append(opts, obiformats.OptionsQualityShift(obiconvert.OutputQualityShift()))
+
+	var formater obiformats.SequenceBatchWriterToFile
+
+	switch obiconvert.OutputFormat() {
+	case "fastq":
+		formater = obiformats.WriteFastqBatchToFile
+	case "fasta":
+		formater = obiformats.WriteFastaBatchToFile
+	default:
+		formater = obiformats.WriteSequencesBatchToFile
+	}
+
+	dispatcher := sequences.Distribute(CLISequenceClassifier(),
+		obioptions.CLIBatchSize())
+
+	obiformats.WriterDispatcher(CLIFileNamePattern(),
+		dispatcher, formater, opts...,
+	)
+
+}

pkg/obitools/obidistribute/options.go

@@ -0,0 +1,58 @@
+package obidistribute
+
+import (
+	"fmt"
+	"log"
+	"strings"
+
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
+	"github.com/DavidGamba/go-getoptions"
+)
+
+var _FilenamePattern = ""
+var _SequenceClassifierTag = ""
+var _BatchCount = 0
+
+func DistributeOptionSet(options *getoptions.GetOpt) {
+	options.StringVar(&_FilenamePattern, "pattern", _FilenamePattern,
+		options.Alias("p"),
+		options.Required("You must provide at pattern for the file names "),
+		options.Description("The N first sequence records of the file are discarded from the analysis and not reported to the output file."))
+
+	options.StringVar(&_SequenceClassifierTag, "classifier", _SequenceClassifierTag,
+		options.Alias("c"),
+		options.Description("The N first sequence records of the file are discarded from the analysis and not reported to the output file."))
+
+	options.IntVar(&_BatchCount, "batch", 0,
+		options.Alias("n"),
+		options.Description("The N first sequence records of the file are discarded from the analysis and not reported to the output file."))
+}
+
+func OptionSet(options *getoptions.GetOpt) {
+	obiconvert.InputOptionSet(options)
+	obiconvert.OutputOptionSet(options)
+	DistributeOptionSet(options)
+}
+
+func CLISequenceClassifier() obiseq.SequenceClassifier {
+	switch {
+	case _SequenceClassifierTag != "":
+		return obiseq.AnnotationClassifier(_SequenceClassifierTag)
+	case _BatchCount > 0:
+		return obiseq.RotateClassifier(_BatchCount)
+
+	}
+
+	log.Fatal("one of the options --classifier or --batch must be specified")
+	return nil
+}
+
+func CLIFileNamePattern() string {
+	x := fmt.Sprintf(_FilenamePattern, "_xxx_")
+	if strings.Contains(x, "(string=_xxx_)") {
+		log.Panicf("patern %s is not correct : %s", _FilenamePattern, x)
+	}
+
+	return _FilenamePattern
+}

pkg/obitools/obipairing/options.go

@@ -18,10 +18,12 @@ func PairingOptionSet(options *getoptions.GetOpt) {
 	options.StringSliceVar(&_ForwardFiles, "forward-reads",
 		1, 1000,
 		options.Alias("F"),
+		options.Required("You must provide at least one forward file"),
 		options.Description("The file names containing the forward reads"))
 	options.StringSliceVar(&_ReverseFiles, "reverse-reads",
 		1, 1000,
 		options.Alias("R"),
+		options.Required("You must provide at least one reverse file"),
 		options.Description("The file names containing the reverse reads"))
 	options.IntVar(&_Delta, "delta", _Delta,
 		options.Alias("D"),