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Refactor rope scanner and add FASTQ rope parser

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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.
This commit is contained in:
Eric Coissac
2026-03-10 16:46:53 +01:00
parent 623116ab13
commit 3d2e205722
5 changed files with 176 additions and 83 deletions
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4
pkg/obiformats/fastaseq_read.go
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@@ -214,7 +214,7 @@ func FastaChunkParser(UtoT bool) func(string, io.Reader) (obiseq.BioSequenceSlic
// Stops when '>' is found at the start of a line (next record) or at EOF.
// Returns (dest with appended bases, hasMore).
// hasMore=true means scanner is now positioned at '>' of the next record.
func (s *gbRopeScanner) extractFastaSeq(dest []byte, UtoT bool) ([]byte, bool) {
func (s *ropeScanner) extractFastaSeq(dest []byte, UtoT bool) ([]byte, bool) {
lineStart := true
for s.current != nil {
@@ -252,7 +252,7 @@ func (s *gbRopeScanner) extractFastaSeq(dest []byte, UtoT bool) ([]byte, bool) {
// FastaChunkParserRope parses a FASTA chunk directly from the rope without Pack().
func FastaChunkParserRope(source string, rope *PieceOfChunk, UtoT bool) (obiseq.BioSequenceSlice, error) {
scanner := newGbRopeScanner(rope)
scanner := newRopeScanner(rope)
sequences := obiseq.MakeBioSequenceSlice(100)[:0]
for {