Go implementation of fasta and fastq parser

Former-commit-id: 3f4fd355c169afbef2d5fef1f5e407aabb71d031

pkg/obiformats/fastaseq_read.go

@@ -16,7 +16,7 @@ import (
 	log "github.com/sirupsen/logrus"
 )
 
-// lastSequenceCut extracts the up to the last sequence cut from a given buffer.
+// lastFastaCut extracts the up to the last sequence cut from a given buffer.
 //
 // It takes a parameter:
 //   - buffer []byte: the buffer to extract the sequence cut from.
@@ -24,7 +24,7 @@ import (
 // It returns two values:
 //   - []byte: the extracted sequences.
 //   - []byte: the remaining buffer after the sequence cut (the last sequence).
-func lastSequenceCut(buffer []byte) ([]byte, []byte) {
+func lastFastaCut(buffer []byte) ([]byte, []byte) {
 	imax := len(buffer)
 	last := 0
 	state := 0
@@ -45,13 +45,13 @@ func lastSequenceCut(buffer []byte) ([]byte, []byte) {
 	return []byte{}, buffer
 }
 
-// firstSequenceCut cuts the input buffer at the first occurrence of a ">" character
+// firstFastaCut cuts the input buffer at the first occurrence of a ">" character
 // following a sequence of "\r" or "\n" characters.
 //
 // It takes a byte slice as input, representing the buffer to be cut.
 // It returns two byte slices: the first slice contains the part of the buffer before the cut,
 // and the second slice contains the part of the buffer after the cut.
-func firstSequenceCut(buffer []byte) ([]byte, []byte) {
+func firstFastaCut(buffer []byte) ([]byte, []byte) {
 	imax := len(buffer)
 	last := 0
 	state := 0
@@ -73,17 +73,6 @@ func firstSequenceCut(buffer []byte) ([]byte, []byte) {
 
 }
 
-func fullSequenceCut(buffer []byte) ([]byte, []byte, []byte) {
-	before, buffer := firstSequenceCut(buffer)
-
-	if len(buffer) == 0 {
-		return before, []byte{}, []byte{}
-	}
-
-	buffer, after := lastSequenceCut(buffer)
-	return before, buffer, after
-}
-
 func Concatenate[S ~[]E, E any](s1, s2 S) S {
 	if len(s1) > 0 {
 		if len(s2) > 0 {
@@ -109,7 +98,7 @@ func FastaChunkReader(r io.Reader, size int, cutHead bool) (chan FastxChunk, err
 			buff = buff[:n]
 		}
 
-		begin, buff := firstSequenceCut(buff)
+		begin, buff := firstFastaCut(buff)
 
 		if len(begin) > 0 && !cutHead {
 			return out, fmt.Errorf("begin is not empty : %s", string(begin))
@@ -127,7 +116,7 @@ func FastaChunkReader(r io.Reader, size int, cutHead bool) (chan FastxChunk, err
 				buff = Concatenate(end, buff)
 				// fmt.Println("------------buff--pasted----------------")
 				// fmt.Println(string(buff))
-				buff, end = lastSequenceCut(buff)
+				buff, end = lastFastaCut(buff)
 				// fmt.Println("----------------buff--cutted------------")
 				// fmt.Println(string(buff))
 				// fmt.Println("------------------end-------------------")