Eric Coissac
cfadf63bbc
Replace the existing chunk and Rope-based processing pipeline with a fixed-size NucPage architecture. Introduce a new nucstream module featuring buffer-pooled, in-place parsing that auto-detects and decompresses FASTA/FASTQ/GenBank inputs into normalized ACGT streams with k-mer overlap preservation. Update obikmer scatter and superkmer stages to consume NucPage iterators and cursor-based navigation, eliminating std::io::Read dependencies and optimizing memory management. Add a configurable max_open_files CLI argument and update implementation documentation to reflect the new record vs. stream reading paths.
110 lines
4.9 KiB
Markdown
110 lines
4.9 KiB
Markdown
# Chunk reader — implementation
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`obiread` exposes two distinct sequence reading paths, each optimised for a different use case.
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## Two reading paths
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| Path | API | Output unit | Per-record identity | Use case |
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|------|-----|-------------|---------------------|----------|
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| **Record path** | `read_sequence_chunks` → `parse_chunk` | `SeqRecord` (id + raw sequence + normalised rope) | yes | `query` — must read complete records |
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| **Stream path** | `open_nuc_stream` | `NucPage` (flat normalised byte buffer) | no | `index`, `superkmer` — bulk throughput |
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The record path uses `Rope`-backed chunks and is described in detail below.
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The stream path (`NucStream` / `NucPage`) is described in the scatter section of [pipeline](pipeline.md).
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---
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## Record path: chunk reader
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The chunk reader reads FASTA or FASTQ files in fixed-size blocks and yields self-contained chunks, each ending on a complete sequence record boundary. `parse_chunk` then converts each chunk into a `Vec<SeqRecord>`, where each record carries its identifier, raw sequence bytes, and a normalised rope ready for superkmer building.
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This path is mandatory for `query`, where superkmers must be tracked back to their originating sequence (id, kmer offset) for output annotation.
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## Output type: Rope
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Each chunk is a `Rope` — a segmented byte sequence: a `Vec` of blocks, where each block is a `Vec<Cell<u8>>`. The consumer iterates over the blocks via a forward or backward cursor.
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`Rope::split_off(pos)` splits at an absolute byte offset in O(log n) (binary search over block-start index). If `pos` falls inside a block, that block is split in two via `Vec::split_off` — no `memcpy` in the common case.
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## SeqChunkIter
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```rust
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pub struct SeqChunkIter<R: Read> { /* private */ }
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impl<R: Read> Iterator for SeqChunkIter<R> {
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type Item = io::Result<Rope>;
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}
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pub fn fasta_chunks<R: Read>(source: R) -> SeqChunkIter<R>
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pub fn fastq_chunks<R: Read>(source: R) -> SeqChunkIter<R>
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```
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`next()` loop:
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```text
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1. read one block of block_size bytes → push onto Rope
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2. call splitter(rope) → Option<abs_offset>
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if Some(pos):
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tail = rope.split_off(pos) ← O(log n), may split one block
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chunk = mem::replace(&mut rope, tail)
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return Some(Ok(chunk))
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3. if EOF and rope non-empty: return Some(Ok(rope)) as final chunk
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4. if EOF and rope empty: return None
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```
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The `Splitter` function signature is `fn(&Rope) -> Option<usize>`. It returns the absolute byte offset of the start of the last complete record, or `None` if no boundary was found in the accumulated rope (need more data).
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## Boundary detection — FASTA
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Backward scan with a 2-state machine. Searches (right to left) for `>` followed by `\n` or `\r` (i.e., a `>` that is preceded by a newline in forward order):
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```mermaid
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stateDiagram-v2
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direction LR
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[*] --> Scanning
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Scanning --> FoundGt : '>'
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FoundGt --> Scanning : other
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FoundGt --> [*] : '\\n' / '\\r' ✓
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```
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Returns the byte offset of the `>` that starts the last complete record. Returns `None` if only one `>` is found (cannot confirm there is a prior complete record).
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## Boundary detection — FASTQ
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FASTQ records have a rigid 4-line structure (`@header`, sequence, `+`, quality). The `@` character (ASCII 64, Phred score 31) can appear legitimately in quality lines, making any forward heuristic unreliable. The backward scanner verifies the full structural context before accepting a candidate `@`.
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7-state machine (states 0–6), scanning from **right to left**. Each time a `+` is found, its position is saved as `restart`; any state mismatch resets the scan to that position.
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```mermaid
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stateDiagram-v2
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direction LR
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[*] --> Scanning
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Scanning --> FoundPlus : '+' (save restart)
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FoundPlus --> AfterNlPlus : '\\n' / '\\r'
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FoundPlus --> Scanning : other → backtrack
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AfterNlPlus --> AfterNlPlus : séparateur
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AfterNlPlus --> InSequence : lettre / - / . / [ / ]
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AfterNlPlus --> Scanning : other → backtrack
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InSequence --> AfterSequence : '\\n' / '\\r'
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InSequence --> InSequence : lettre / - / . / [ / ]
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InSequence --> Scanning : other → backtrack
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AfterSequence --> AfterSequence : '\\n' / '\\r'
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AfterSequence --> InHeader : other
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InHeader --> FoundAt : '@' (save cut)
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InHeader --> Scanning : '\\n' / '\\r' → backtrack
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InHeader --> InHeader : other
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FoundAt --> [*] : '\\n' / '\\r' ✓
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FoundAt --> InHeader : other
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```
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`restart` is updated each time a `+` is found. When any state fails its expected input, the scan jumps back to `restart` and continues from there — guaranteeing that a `@` in a quality line cannot be accepted as a record start, because the `\n+\n` structure immediately following it (going backward) will not be found.
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Returns the byte offset of the `@` that starts the last complete record.
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