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Patch the empty batch bug

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Former-commit-id: fcee04b58f2c4a0bf2c27792f991391c0b6ce78e
This commit is contained in:
Eric Coissac
2023-03-07 20:16:06 +07:00
parent 1e7756ec91
commit 5fbe52368c
6 changed files with 11 additions and 35 deletions
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1
pkg/obiformats/fastseq_write_fasta.go
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@ -69,6 +69,7 @@ func WriteFasta(iterator obiiter.IBioSequence,
options ...WithOption) (obiiter.IBioSequence, error) { options ...WithOption) (obiiter.IBioSequence, error) {
opt := MakeOptions(options) opt := MakeOptions(options)
iterator = iterator.Rebatch(10000)
file, _ = goutils.CompressStream(file, opt.CompressedFile(), opt.CloseFile()) file, _ = goutils.CompressStream(file, opt.CompressedFile(), opt.CloseFile())
newIter := obiiter.MakeIBioSequence() newIter := obiiter.MakeIBioSequence()

3
pkg/obiformats/fastseq_write_fastq.go
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@ -56,6 +56,9 @@ type FileChunck struct {
func WriteFastq(iterator obiiter.IBioSequence, func WriteFastq(iterator obiiter.IBioSequence,
file io.WriteCloser, file io.WriteCloser,
options ...WithOption) (obiiter.IBioSequence, error) { options ...WithOption) (obiiter.IBioSequence, error) {
iterator = iterator.Rebatch(10000)
opt := MakeOptions(options) opt := MakeOptions(options)
file, _ = goutils.CompressStream(file, opt.CompressedFile(), opt.CloseFile()) file, _ = goutils.CompressStream(file, opt.CompressedFile(), opt.CloseFile())

2
pkg/obiformats/universal_write.go
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@ -14,8 +14,6 @@ func WriteSequence(iterator obiiter.IBioSequence,
file io.WriteCloser, file io.WriteCloser,
options ...WithOption) (obiiter.IBioSequence, error) { options ...WithOption) (obiiter.IBioSequence, error) {
iterator = iterator.Rebatch(1000)
ok := iterator.Next() ok := iterator.Next()
if ok { if ok {

6
pkg/obiiter/batchiterator.go
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@ -235,9 +235,9 @@ func (iterator IBioSequence) Push(batch BioSequenceBatch) {
if batch.IsNil() { if batch.IsNil() {
log.Panicln("A Nil batch is pushed on the channel") log.Panicln("A Nil batch is pushed on the channel")
} }
if batch.Len() == 0 { // if batch.Len() == 0 {
log.Panicln("An empty batch is pushed on the channel") // log.Panicln("An empty batch is pushed on the channel")
} // }
iterator.pointer.channel <- batch iterator.pointer.channel <- batch
} }

31
pkg/obitools/obiconvert/sequence_reader.go
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@ -138,7 +138,7 @@ func CLIReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
} }
iterator = obiformats.ReadSequencesBatchFromFiles( iterator = obiformats.ReadSequencesBatchFromFiles(
filenames, list_of_files,
reader, reader,
nreader, nreader,
opts..., opts...,
@ -162,34 +162,11 @@ func CLIReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
} }
// list_of_files = list_of_files[1:]
// others := make([]obiiter.IBioSequenceBatch, 0, len(list_of_files))
// for _, fn := range list_of_files {
// r, err := reader(fn, opts...)
// if err != nil {
// return obiiter.NilIBioSequenceBatch, err
// }
// others = append(others, r)
// }
// if len(others) > 0 {
// if CLINoInputOrder() {
// iterator = iterator.Pool(others...)
// } else {
// iterator = iterator.Concat(others...)
// }
// }
} }
// if SequencesToSkip() > 0 { if CLIProgressBar() {
// iterator = iterator.Skip(SequencesToSkip()) iterator = iterator.Speed()
// } }
// if AnalyzeOnly() > 0 {
// iterator = iterator.Head(AnalyzeOnly())
// }
return iterator, nil return iterator, nil
} }

3
pkg/obitools/obiconvert/sequence_writer.go
View File

@ -35,9 +35,6 @@ func BuildPairedFileNames(filename string) (string, string) {
func CLIWriteBioSequences(iterator obiiter.IBioSequence, func CLIWriteBioSequences(iterator obiiter.IBioSequence,
terminalAction bool, filenames ...string) (obiiter.IBioSequence, error) { terminalAction bool, filenames ...string) (obiiter.IBioSequence, error) {
if CLIProgressBar() {
iterator = iterator.Speed()
}
var newIter obiiter.IBioSequence var newIter obiiter.IBioSequence
opts := make([]obiformats.WithOption, 0, 10) opts := make([]obiformats.WithOption, 0, 10)