optimize sequence readers and patch a bug in the format guesser

Former-commit-id: 9dce1e96c57ae9a88c26fac5c8e1bdcdc2c0c7a5

pkg/obiformats/embl_read.go

@@ -192,8 +192,10 @@ func _ReadFlatFileChunk(reader io.Reader, readers chan _FileChunk) {
 	for err == nil {
 
 		// Read from the reader until the buffer is full or the end of the file is reached
-		for ; err == nil && l < len(buff); l += size {
-			size, err = reader.Read(buff[l:])
+		l, err = io.ReadFull(reader, buff)
+
+		if err == io.ErrUnexpectedEOF {
+			err = nil
 		}
 
 		// Create an extended buffer to read from if the end of the last entry is not found in the current buffer
@@ -205,7 +207,7 @@ func _ReadFlatFileChunk(reader io.Reader, readers chan _FileChunk) {
 		// Read from the reader in 1 MB increments until the end of the last entry is found
 		for end = _EndOfLastEntry(buff); err == nil && end < 0; end = _EndOfLastEntry(extbuff[:size]) {
 			ic++
-			size, err = reader.Read(extbuff)
+			size, err = io.ReadFull(reader, extbuff)
 			buff = append(buff, extbuff[:size]...)
 		}
 

pkg/obiformats/fastaseq_read.go

@@ -92,7 +92,12 @@ func FastaChunkReader(r io.Reader, size int, cutHead bool) (chan FastxChunk, err
 	out := make(chan FastxChunk)
 	buff := make([]byte, size)
 
-	n, err := r.Read(buff)
+	n, err := io.ReadFull(r, buff)
+
+	if err == io.ErrUnexpectedEOF {
+		err = nil
+	}
+
 	if n > 0 && err == nil {
 		if n < size {
 			buff = buff[:n]
@@ -128,13 +133,20 @@ func FastaChunkReader(r io.Reader, size int, cutHead bool) (chan FastxChunk, err
 						index: idx,
 					}
 					idx++
+				} else {
+					size = size * 2
 				}
 
 				buff = slices.Grow(buff[:0], size)[0:size]
-				n, err = r.Read(buff)
+				n, err = io.ReadFull(r, buff)
 				if n < size {
 					buff = buff[:n]
 				}
+
+				if err == io.ErrUnexpectedEOF {
+					err = nil
+				}
+
 				// fmt.Printf("n = %d, err = %v\n", n, err)
 			}
 

pkg/obiformats/fastqseq_read.go

@@ -99,7 +99,11 @@ func FastqChunkReader(r io.Reader, size int) (chan FastxChunk, error) {
 	out := make(chan FastxChunk)
 	buff := make([]byte, size)
 
-	n, err := r.Read(buff)
+	n, err := io.ReadFull(r, buff)
+
+	if err == io.ErrUnexpectedEOF {
+		err = nil
+	}
 
 	if n > 0 && err == nil {
 		if n < size {
@@ -130,13 +134,19 @@ func FastqChunkReader(r io.Reader, size int) (chan FastxChunk, error) {
 						index: idx,
 					}
 					idx++
+				} else {
+					size = size * 2
 				}
 
 				buff = slices.Grow(buff[:0], size)[0:size]
-				n, err = r.Read(buff)
+				n, err = io.ReadFull(r, buff)
 				if n < size {
 					buff = buff[:n]
 				}
+
+				if err == io.ErrUnexpectedEOF {
+					err = nil
+				}
 				// fmt.Printf("n = %d, err = %v\n", n, err)
 			}
 

pkg/obiformats/universal_read.go

@@ -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
 }