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Patch the fastq detector

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This commit is contained in:
Eric Coissac
2025-08-08 10:23:03 -04:00
parent 7a6d552450
commit 6d204f6281
3 changed files with 8 additions and 2 deletions
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2
pkg/obiformats/ngsfilter_read.go
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@@ -568,6 +568,8 @@ func ReadCSVNGSFilter(reader io.Reader) (*obingslibrary.NGSLibrary, error) {
for i = 0; i < len(records) && records[i][0] == "@param"; i++ { for i = 0; i < len(records) && records[i][0] == "@param"; i++ {
} }
log.Infof("%d parameters found", i)
params := records[0:i] params := records[0:i]
records = records[i:] records = records[i:]

2
pkg/obioptions/version.go
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@@ -8,7 +8,7 @@ import (
// corresponds to the last commit, and not the one when the file will be // corresponds to the last commit, and not the one when the file will be
// commited // commited
var _Commit = "730d448" var _Commit = "7a6d552"
var _Version = "Release 4.4.0" var _Version = "Release 4.4.0"
// Version returns the version of the obitools package. // Version returns the version of the obitools package.

6
pkg/obiutils/mimetypes.go
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@@ -78,7 +78,11 @@ func RegisterOBIMimeType() {
} }
fastqDetector := func(raw []byte, limit uint32) bool { fastqDetector := func(raw []byte, limit uint32) bool {
ok, err := regexp.Match("^@[^ ].*\n[A-Za-z.-]+\n\\+", raw) ok, err := regexp.Match("^@[^ ].*\n[A-Za-z.-]+", raw)
if ok && err == nil {
ok, err = regexp.Match("^@param,[^ ]", raw)
ok = !ok
}
return ok && err == nil return ok && err == nil
} }