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Change the way sequence definition are managed. They are now when present stored as an attribute

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Former-commit-id: 6e618377c05b42937d2eace3c9668390980ab68c
This commit is contained in:
Eric Coissac
2023-10-05 07:21:12 +02:00
parent 5c30ec354f
commit d23a911080
11 changed files with 115 additions and 30 deletions
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10
pkg/obiformats/fastqseq_read.go
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@@ -339,6 +339,11 @@ func ReadFastqFromFile(filename string, options ...WithOption) (obiiter.IBioSequ
file, err := Ropen(filename)
if err == ErrNoContent {
log.Infof("file %s is empty", filename)
return ReadEmptyFile(options...)
}
if err != nil {
return obiiter.NilIBioSequence, err
}
@@ -350,6 +355,11 @@ func ReadFastqFromStdin(reader io.Reader, options ...WithOption) (obiiter.IBioSe
options = append(options, OptionsSource(obiutils.RemoveAllExt("stdin")))
input, err := Buf(os.Stdin)
if err == ErrNoContent {
log.Infof("stdin is empty")
return ReadEmptyFile(options...)
}
if err != nil {
log.Fatalf("open file error: %v", err)
return obiiter.NilIBioSequence, err