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Adds the ability to read gzip-tar file for the taxonomy dump

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This commit is contained in:
Eric Coissac
2025-01-24 11:47:59 +01:00
parent ffd67252c3
commit 3137c1f841
17 changed files with 305 additions and 64 deletions
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8
pkg/obiformats/fastqseq_read.go
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@@ -370,9 +370,9 @@ func ReadFastq(reader io.Reader, options ...WithOption) (obiiter.IBioSequence, e
func ReadFastqFromFile(filename string, options ...WithOption) (obiiter.IBioSequence, error) {
options = append(options, OptionsSource(obiutils.RemoveAllExt((path.Base(filename)))))
file, err := Ropen(filename)
file, err := obiutils.Ropen(filename)
if err == ErrNoContent {
if err == obiutils.ErrNoContent {
log.Infof("file %s is empty", filename)
return ReadEmptyFile(options...)
}
@@ -386,9 +386,9 @@ func ReadFastqFromFile(filename string, options ...WithOption) (obiiter.IBioSequ
func ReadFastqFromStdin(reader io.Reader, options ...WithOption) (obiiter.IBioSequence, error) {
options = append(options, OptionsSource(obiutils.RemoveAllExt("stdin")))
input, err := Buf(os.Stdin)
input, err := obiutils.Buf(os.Stdin)
if err == ErrNoContent {
if err == obiutils.ErrNoContent {
log.Infof("stdin is empty")
return ReadEmptyFile(options...)
}