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Remove single sequence ierators. Only batch iterators persist

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This commit is contained in:
Eric Coissac
2022-11-16 10:58:59 +01:00
parent f674200a6e
commit 6f853da9df
14 changed files with 4 additions and 651 deletions
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6
pkg/obitools/obiconvert/sequence_reader.go
View File

@@ -175,9 +175,3 @@ func ReadBioSequencesBatch(filenames ...string) (obiiter.IBioSequenceBatch, erro
return iterator, nil
}
func ReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
ib, err := ReadBioSequencesBatch(filenames...)
return ib.SortBatches().IBioSequence(), err
}

57
pkg/obitools/obiconvert/sequence_writer.go
View File

@@ -8,63 +8,6 @@ import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
)
func WriteBioSequences(iterator obiiter.IBioSequence, filenames ...string) error {
opts := make([]obiformats.WithOption, 0, 10)
switch CLIOutputFastHeaderFormat() {
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(CLIOutputQualityShift()))
var err error
if len(filenames) == 0 {
switch CLIOutputFormat() {
case "fastq":
err = obiformats.WriteFastqToStdout(iterator, opts...)
case "fasta":
err = obiformats.WriteFastaToStdout(iterator, opts...)
default:
err = obiformats.WriteSequencesToStdout(iterator, opts...)
}
} else {
switch CLIOutputFormat() {
case "fastq":
err = obiformats.WriteFastqToFile(iterator, filenames[0], opts...)
case "fasta":
err = obiformats.WriteFastaToFile(iterator, filenames[0], opts...)
default:
err = obiformats.WriteSequencesToFile(iterator, filenames[0], opts...)
}
}
if err != nil {
log.Fatalf("Write file error: %v", err)
return err
}
return nil
}
func WriteBioSequencesBatch(iterator obiiter.IBioSequenceBatch,
terminalAction bool, filenames ...string) (obiiter.IBioSequenceBatch, error) {