mirror of
https://github.com/metabarcoding/obitools4.git
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3d2e205722
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.
81 lines
1.8 KiB
Go
81 lines
1.8 KiB
Go
package obiformats
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import "bytes"
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// ropeScanner reads lines from a PieceOfChunk rope without heap allocation.
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// The carry buffer (stack) handles lines that span two rope nodes.
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type ropeScanner struct {
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current *PieceOfChunk
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pos int
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carry [256]byte // 256 gives ample margin for typical flat-file lines
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carryN int
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}
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func newRopeScanner(rope *PieceOfChunk) *ropeScanner {
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return &ropeScanner{current: rope}
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}
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// ReadLine returns the next line without the trailing \n (or \r\n).
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// Returns nil at end of rope. The returned slice aliases carry[] or the node
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// data and is valid only until the next ReadLine call.
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func (s *ropeScanner) ReadLine() []byte {
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for {
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if s.current == nil {
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if s.carryN > 0 {
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n := s.carryN
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s.carryN = 0
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return s.carry[:n]
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}
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return nil
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}
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data := s.current.data[s.pos:]
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idx := bytes.IndexByte(data, '\n')
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if idx >= 0 {
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var line []byte
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if s.carryN == 0 {
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line = data[:idx]
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} else {
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n := copy(s.carry[s.carryN:], data[:idx])
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s.carryN += n
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line = s.carry[:s.carryN]
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s.carryN = 0
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}
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s.pos += idx + 1
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if s.pos >= len(s.current.data) {
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s.current = s.current.Next()
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s.pos = 0
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}
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if len(line) > 0 && line[len(line)-1] == '\r' {
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line = line[:len(line)-1]
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}
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return line
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}
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// No \n in this node: accumulate into carry and advance
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n := copy(s.carry[s.carryN:], data)
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s.carryN += n
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s.current = s.current.Next()
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s.pos = 0
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}
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}
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// skipToNewline advances the scanner past the next '\n'.
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func (s *ropeScanner) skipToNewline() {
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for s.current != nil {
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data := s.current.data[s.pos:]
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idx := bytes.IndexByte(data, '\n')
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if idx >= 0 {
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s.pos += idx + 1
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if s.pos >= len(s.current.data) {
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s.current = s.current.Next()
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s.pos = 0
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}
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return
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}
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s.current = s.current.Next()
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s.pos = 0
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}
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}
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