obitools/obitools4
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Changes to be committed:

Browse Source 
modified:   pkg/obiformats/universal_read.go
	modified:   pkg/obioptions/version.go
	modified:   pkg/obiseq/taxonomy_methods.go
This commit is contained in:
Eric Coissac
2025-02-12 08:40:38 +01:00
parent 6a8061cc4f
commit 4774438644
3 changed files with 6 additions and 7 deletions
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2
pkg/obiformats/universal_read.go
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@ -72,7 +72,7 @@ func OBIMimeTypeGuesser(stream io.Reader) (*mimetype.MIME, io.Reader, error) {
}
fastqDetector := func(raw []byte, limit uint32) bool {
ok, err := regexp.Match("^@[^ ].*\n[^ ]+\n\\+", raw)
ok, err := regexp.Match("^@[^ ].*\n[A-Za-z.-]+", raw)
return ok && err == nil
}

2
pkg/obioptions/version.go
View File

@ -8,7 +8,7 @@ import (
// corresponds to the last commit, and not the one when the file will be
// commited
var _Commit = "e2563cd"
var _Commit = "6a8061c"
var _Version = "Release 4.2.0"
// Version returns the version of the obitools package.

9
pkg/obiseq/taxonomy_methods.go
View File

@ -41,13 +41,12 @@ func (s *BioSequence) SetTaxid(taxid string, rank ...string) {
taxon, isAlias, err = taxonomy.Taxon(taxid)
if err != nil {
logger := log.Warnf
if obidefault.FailOnTaxonomy() {
log.Fatalf("%s: Taxid: %v is unknown from taxonomy (%v)",
s.Id(), taxid, err)
} else {
log.Warnf("%s: Taxid: %v is unknown from taxonomy (%v)",
s.Id(), taxid, err)
logger = log.Fatalf
}
logger("%s: Taxid: %v is unknown from taxonomy (%v)",
s.Id(), taxid, err)
}
if isAlias {