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optimize sequence readers and patch a bug in the format guesser

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Former-commit-id: 9dce1e96c57ae9a88c26fac5c8e1bdcdc2c0c7a5
This commit is contained in:
Eric Coissac
2023-10-13 21:52:57 +02:00
parent ddf0f2cede
commit e8c55a2b6b
7 changed files with 141 additions and 46 deletions
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16
pkg/obiformats/universal_read.go
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@ -69,11 +69,17 @@ func OBIMimeTypeGuesser(stream io.Reader) (*mimetype.MIME, io.Reader, error) {
mimetype.Lookup("text/plain").Extend(genbankDetector, "text/genbank", ".seq")
mimetype.Lookup("text/plain").Extend(emblDetector, "text/embl", ".dat")
mimetype.Lookup("application/octet-stream").Extend(fastaDetector, "text/fasta", ".fasta")
mimetype.Lookup("application/octet-stream").Extend(fastqDetector, "text/fastq", ".fastq")
mimetype.Lookup("application/octet-stream").Extend(ecoPCR2Detector, "text/ecopcr2", ".ecopcr")
mimetype.Lookup("application/octet-stream").Extend(genbankDetector, "text/genbank", ".seq")
mimetype.Lookup("application/octet-stream").Extend(emblDetector, "text/embl", ".dat")
// Create a buffer to store the read data
buf := make([]byte, 1024*128)
n, err := stream.Read(buf)
n, err := io.ReadFull(stream, buf)
if err != nil && err != io.EOF {
if err != nil && err != io.ErrUnexpectedEOF {
return nil, nil, err
}
@ -84,7 +90,11 @@ func OBIMimeTypeGuesser(stream io.Reader) (*mimetype.MIME, io.Reader, error) {
}
// Create a new reader based on the read data
newReader := io.MultiReader(bytes.NewReader(buf[:n]), stream)
newReader := io.Reader(bytes.NewReader(buf[:n]))
if err == nil {
newReader = io.MultiReader(newReader, stream)
}
return mimeType, newReader, nil
}