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Patch reading of annotation from stdin

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This commit is contained in:
Eric Coissac
2022-09-29 14:48:05 +02:00
parent d0f63fda56
commit 65210755cc
3 changed files with 17 additions and 5 deletions
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6
pkg/obitools/obiconvert/sequence_reader.go
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@@ -82,7 +82,7 @@ func ReadBioSequencesBatch(filenames ...string) (obiiter.IBioSequenceBatch, erro
opts = append(opts, obiformats.OptionsFastSeqHeaderParser(obiformats.ParseGuessedFastSeqHeader))
}
nworkers := obioptions.CLIParallelWorkers() / 4
nworkers := obioptions.CLIParallelWorkers() // / 4
if nworkers < 2 {
nworkers = 2
}
@@ -94,7 +94,7 @@ func ReadBioSequencesBatch(filenames ...string) (obiiter.IBioSequenceBatch, erro
opts = append(opts, obiformats.OptionsQualityShift(CLIInputQualityShift()))
if len(filenames) == 0 {
log.Printf("Reading sequences from stdin in %s\n", CLIInputFormat())
switch CLIInputFormat() {
case "ecopcr":
iterator = obiformats.ReadEcoPCRBatch(os.Stdin, opts...)
@@ -129,7 +129,7 @@ func ReadBioSequencesBatch(filenames ...string) (obiiter.IBioSequenceBatch, erro
if CLINoInputOrder() {
nreader = obioptions.CLIParallelWorkers()
}
iterator = obiformats.ReadSequencesBatchFromFiles(
filenames,
reader,