Refactor rope scanner and add FASTQ rope parser

This commit refactors the rope scanner implementation by renaming gbRopeScanner to ropeScanner and extracting the common functionality into a new file. It also introduces a new FastqChunkParserRope function that parses FASTQ chunks directly from a rope without Pack(), enabling more efficient memory usage. The existing parsers are updated to use the new rope-based parser when available. The BioSequence type is enhanced with a TakeQualities method for more efficient quality data handling.

pkg/obiformats/rope_scanner.go

@@ -0,0 +1,80 @@
+package obiformats
+
+import "bytes"
+
+// ropeScanner reads lines from a PieceOfChunk rope without heap allocation.
+// The carry buffer (stack) handles lines that span two rope nodes.
+type ropeScanner struct {
+	current *PieceOfChunk
+	pos     int
+	carry   [256]byte // 256 gives ample margin for typical flat-file lines
+	carryN  int
+}
+
+func newRopeScanner(rope *PieceOfChunk) *ropeScanner {
+	return &ropeScanner{current: rope}
+}
+
+// ReadLine returns the next line without the trailing \n (or \r\n).
+// Returns nil at end of rope. The returned slice aliases carry[] or the node
+// data and is valid only until the next ReadLine call.
+func (s *ropeScanner) ReadLine() []byte {
+	for {
+		if s.current == nil {
+			if s.carryN > 0 {
+				n := s.carryN
+				s.carryN = 0
+				return s.carry[:n]
+			}
+			return nil
+		}
+
+		data := s.current.data[s.pos:]
+		idx := bytes.IndexByte(data, '\n')
+
+		if idx >= 0 {
+			var line []byte
+			if s.carryN == 0 {
+				line = data[:idx]
+			} else {
+				n := copy(s.carry[s.carryN:], data[:idx])
+				s.carryN += n
+				line = s.carry[:s.carryN]
+				s.carryN = 0
+			}
+			s.pos += idx + 1
+			if s.pos >= len(s.current.data) {
+				s.current = s.current.Next()
+				s.pos = 0
+			}
+			if len(line) > 0 && line[len(line)-1] == '\r' {
+				line = line[:len(line)-1]
+			}
+			return line
+		}
+
+		// No \n in this node: accumulate into carry and advance
+		n := copy(s.carry[s.carryN:], data)
+		s.carryN += n
+		s.current = s.current.Next()
+		s.pos = 0
+	}
+}
+
+// skipToNewline advances the scanner past the next '\n'.
+func (s *ropeScanner) skipToNewline() {
+	for s.current != nil {
+		data := s.current.data[s.pos:]
+		idx := bytes.IndexByte(data, '\n')
+		if idx >= 0 {
+			s.pos += idx + 1
+			if s.pos >= len(s.current.data) {
+				s.current = s.current.Next()
+				s.pos = 0
+			}
+			return
+		}
+		s.current = s.current.Next()
+		s.pos = 0
+	}
+}