add some doc about optimisation for query
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Eric Coissac
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Layer\<D> — raw mapping, iteration, and batch access
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<a href="#raw-kmer-slot-mapping" class="md-nav__link">
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Raw kmer → slot mapping
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Kmer iteration
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<a href="#batch-lookup-on-payload-vectorsviews" class="md-nav__link">
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<span class="md-ellipsis">
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Batch lookup on payload vectors/views
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sub_matrix / fill_sub_matrix
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<a href="../benchmark_query_testing/" class="md-nav__link">
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<span class="md-ellipsis">
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Benchmark: query-path testing
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<a href="#layerd-raw-mapping-iteration-and-batch-access" class="md-nav__link">
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<span class="md-ellipsis">
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Layer\<D> — raw mapping, iteration, and batch access
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</span>
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<nav class="md-nav" aria-label="Layer\<D> — raw mapping, iteration, and batch access">
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<a href="#raw-kmer-slot-mapping" class="md-nav__link">
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<span class="md-ellipsis">
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Raw kmer → slot mapping
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</span>
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</a>
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<a href="#kmer-iteration" class="md-nav__link">
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<span class="md-ellipsis">
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Kmer iteration
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<a href="#batch-lookup-on-payload-vectorsviews" class="md-nav__link">
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<span class="md-ellipsis">
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Batch lookup on payload vectors/views
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</span>
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</a>
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<a href="#sub_matrix-fill_sub_matrix" class="md-nav__link">
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<span class="md-ellipsis">
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sub_matrix / fill_sub_matrix
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@@ -2000,6 +2150,38 @@
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</code></pre></div>
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<p>Mode 3 (<code>PersistentBitMatrix</code>) has no <code>push_layer</code> on <code>LayeredMap</code>; callers build directly via <code>Layer<PersistentBitMatrix>::build_presence</code>.</p>
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<hr />
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<h2 id="layerd-raw-mapping-iteration-and-batch-access">Layer\<D> — raw mapping, iteration, and batch access</h2>
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<p>Beyond <code>query</code>/<code>find</code> (membership-checked), <code>Layer<D></code> exposes lower-level access used by consumers that already know a kmer is in the layer (e.g. cross-partition sibling resolution) or that need to sweep every kmer/slot without paying for a membership check each time.</p>
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<h3 id="raw-kmer-slot-mapping">Raw kmer → slot mapping</h3>
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<div class="highlight"><pre><span></span><code><span class="k">pub</span><span class="w"> </span><span class="k">fn</span><span class="w"> </span><span class="nf">index</span><span class="p">(</span><span class="o">&</span><span class="bp">self</span><span class="p">,</span><span class="w"> </span><span class="n">kmer</span><span class="p">:</span><span class="w"> </span><span class="nc">CanonicalKmer</span><span class="p">)</span><span class="w"> </span><span class="p">-></span><span class="w"> </span><span class="kt">usize</span>
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<span class="nc">pub</span><span class="w"> </span><span class="k">fn</span><span class="w"> </span><span class="nf">index_batch</span><span class="p">(</span><span class="o">&</span><span class="bp">self</span><span class="p">,</span><span class="w"> </span><span class="n">kmers</span><span class="p">:</span><span class="w"> </span><span class="kp">&</span><span class="p">[</span><span class="n">CanonicalKmer</span><span class="p">])</span><span class="w"> </span><span class="p">-></span><span class="w"> </span><span class="nb">Vec</span><span class="o"><</span><span class="kt">usize</span><span class="o">></span>
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</code></pre></div>
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<p>Pure MPHF mapping, no evidence/fingerprint check — equivalent to <code>MphfOnly::index</code>. Only meaningful when the caller already knows <code>kmer</code> belongs to the layer; on an absent kmer the MPHF still returns <em>some</em> slot (undefined, not <code>None</code>).</p>
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<h3 id="kmer-iteration">Kmer iteration</h3>
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<p>Four iterators, all built from <code>unitigs.bin</code> (physical layout order, <strong>not</strong> correlated with MPHF slot numbers):</p>
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<div class="highlight"><pre><span></span><code><span class="k">pub</span><span class="w"> </span><span class="k">fn</span><span class="w"> </span><span class="nf">iter_kmers</span><span class="p">(</span><span class="o">&</span><span class="bp">self</span><span class="p">)</span><span class="w"> </span><span class="p">-></span><span class="w"> </span><span class="nc">KmerIter</span><span class="o"><'</span><span class="nb">_</span><span class="o">></span>
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<span class="k">pub</span><span class="w"> </span><span class="k">fn</span><span class="w"> </span><span class="nf">enumerate_kmers</span><span class="p">(</span><span class="o">&</span><span class="bp">self</span><span class="p">)</span><span class="w"> </span><span class="p">-></span><span class="w"> </span><span class="nc">Enumerate</span><span class="o"><</span><span class="n">KmerIter</span><span class="o"><'</span><span class="nb">_</span><span class="o">>></span><span class="w"> </span><span class="c1">// (order_index, kmer)</span>
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<span class="k">pub</span><span class="w"> </span><span class="k">fn</span><span class="w"> </span><span class="nf">iter_kmers_batch</span><span class="p">(</span><span class="o">&</span><span class="bp">self</span><span class="p">,</span><span class="w"> </span><span class="n">n</span><span class="p">:</span><span class="w"> </span><span class="kt">usize</span><span class="p">)</span><span class="w"> </span><span class="p">-></span><span class="w"> </span><span class="nc">KmerBatchIter</span><span class="o"><'</span><span class="nb">_</span><span class="o">></span><span class="w"> </span><span class="c1">// Vec<CanonicalKmer> of size ≤ n</span>
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<span class="k">pub</span><span class="w"> </span><span class="k">fn</span><span class="w"> </span><span class="nf">enumerate_kmers_batch</span><span class="p">(</span><span class="o">&</span><span class="bp">self</span><span class="p">,</span><span class="w"> </span><span class="n">n</span><span class="p">:</span><span class="w"> </span><span class="kt">usize</span><span class="p">)</span><span class="w"> </span><span class="p">-></span><span class="w"> </span><span class="nc">impl</span><span class="w"> </span><span class="nb">Iterator</span><span class="o"><</span><span class="n">Item</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">(</span><span class="kt">usize</span><span class="p">,</span><span class="w"> </span><span class="nb">Vec</span><span class="o"><</span><span class="n">CanonicalKmer</span><span class="o">></span><span class="p">)</span><span class="o">></span><span class="w"> </span><span class="o">+</span><span class="w"> </span><span class="nb">Send</span><span class="w"> </span><span class="o">+</span><span class="w"> </span><span class="o">'</span><span class="nb">static</span>
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</code></pre></div>
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<p><code>KmerIter</code>/<code>KmerBatchIter</code> own a clone of the underlying <code>Arc<UnitigFileReader></code> rather than borrowing <code>self</code> — <code>Send + 'static</code>, streamed from disk one kmer at a time, never materialised as a whole. Multiple instances can coexist concurrently, each with its own cursor. <code>enumerate_kmers_batch</code>'s index is the batch's starting offset in iteration order (a multiple of <code>n</code> except for the final, possibly shorter, batch).</p>
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<h3 id="batch-lookup-on-payload-vectorsviews">Batch lookup on payload vectors/views</h3>
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<p><code>PersistentCompactIntVec</code>, <code>PersistentBitVec</code>, <code>IntSliceView</code>, <code>BitSliceView</code> all expose:</p>
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<div class="highlight"><pre><span></span><code><span class="k">fn</span><span class="w"> </span><span class="nf">get_batch</span><span class="p">(</span><span class="o">&</span><span class="bp">self</span><span class="p">,</span><span class="w"> </span><span class="n">slots</span><span class="p">:</span><span class="w"> </span><span class="kp">&</span><span class="p">[</span><span class="kt">usize</span><span class="p">])</span><span class="w"> </span><span class="p">-></span><span class="w"> </span><span class="nb">Vec</span><span class="o"><</span><span class="n">T</span><span class="o">></span>
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<span class="k">fn</span><span class="w"> </span><span class="nf">fill_batch</span><span class="p">(</span><span class="o">&</span><span class="bp">self</span><span class="p">,</span><span class="w"> </span><span class="n">slots</span><span class="p">:</span><span class="w"> </span><span class="kp">&</span><span class="p">[</span><span class="kt">usize</span><span class="p">],</span><span class="w"> </span><span class="n">out</span><span class="p">:</span><span class="w"> </span><span class="kp">&</span><span class="nc">mut</span><span class="w"> </span><span class="p">[</span><span class="n">T</span><span class="p">])</span>
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</code></pre></div>
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<p>Both sort <code>slots</code> internally for sequential mmap access, then reorder results back to the caller's original order. <code>fill_batch</code> fills a caller-provided buffer, avoiding the <code>Vec</code> allocation.</p>
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<h3 id="sub_matrix-fill_sub_matrix">sub_matrix / fill_sub_matrix</h3>
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<div class="highlight"><pre><span></span><code><span class="c1">// Layer<PersistentCompactIntMatrix></span>
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<span class="k">pub</span><span class="w"> </span><span class="k">fn</span><span class="w"> </span><span class="nf">sub_matrix</span><span class="p">(</span><span class="o">&</span><span class="bp">self</span><span class="p">,</span><span class="w"> </span><span class="n">slots</span><span class="p">:</span><span class="w"> </span><span class="kp">&</span><span class="p">[</span><span class="kt">usize</span><span class="p">])</span><span class="w"> </span><span class="p">-></span><span class="w"> </span><span class="nb">Vec</span><span class="o"><</span><span class="nb">Vec</span><span class="o"><</span><span class="kt">u32</span><span class="o">>></span><span class="w"> </span><span class="c1">// column-first</span>
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<span class="k">pub</span><span class="w"> </span><span class="k">fn</span><span class="w"> </span><span class="nf">fill_sub_matrix</span><span class="p">(</span><span class="o">&</span><span class="bp">self</span><span class="p">,</span><span class="w"> </span><span class="n">slots</span><span class="p">:</span><span class="w"> </span><span class="kp">&</span><span class="p">[</span><span class="kt">usize</span><span class="p">],</span><span class="w"> </span><span class="n">out</span><span class="p">:</span><span class="w"> </span><span class="kp">&</span><span class="nc">mut</span><span class="w"> </span><span class="p">[</span><span class="nb">Vec</span><span class="o"><</span><span class="kt">u32</span><span class="o">></span><span class="p">])</span>
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<span class="c1">// Layer<PersistentBitMatrix> (and any D: BinaryMatrix, e.g. PersistentSparseBitMatrix)</span>
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<span class="k">pub</span><span class="w"> </span><span class="k">fn</span><span class="w"> </span><span class="nf">sub_matrix</span><span class="p">(</span><span class="o">&</span><span class="bp">self</span><span class="p">,</span><span class="w"> </span><span class="n">slots</span><span class="p">:</span><span class="w"> </span><span class="kp">&</span><span class="p">[</span><span class="kt">usize</span><span class="p">])</span><span class="w"> </span><span class="p">-></span><span class="w"> </span><span class="nb">Vec</span><span class="o"><</span><span class="nb">Vec</span><span class="o"><</span><span class="kt">bool</span><span class="o">>></span>
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<span class="k">pub</span><span class="w"> </span><span class="k">fn</span><span class="w"> </span><span class="nf">fill_sub_matrix</span><span class="p">(</span><span class="o">&</span><span class="bp">self</span><span class="p">,</span><span class="w"> </span><span class="n">slots</span><span class="p">:</span><span class="w"> </span><span class="kp">&</span><span class="p">[</span><span class="kt">usize</span><span class="p">],</span><span class="w"> </span><span class="n">out</span><span class="p">:</span><span class="w"> </span><span class="kp">&</span><span class="nc">mut</span><span class="w"> </span><span class="p">[</span><span class="nb">Vec</span><span class="o"><</span><span class="kt">bool</span><span class="o">></span><span class="p">])</span>
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</code></pre></div>
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<p>Column-first to match the on-disk column-major layout. <code>fill_sub_matrix</code> sorts <code>slots</code> once, then calls each column's <code>fill_batch</code> in turn — no redundant per-column sort. On <code>PersistentSparseBitMatrix</code> (k-mer-major, no column method) this degrades to a row-by-row decode; see <a href="../../architecture/siblings/">siblings.md</a>.</p>
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<h2 id="layeredstores-and-aggregation-traits">LayeredStore\<S> and aggregation traits</h2>
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<p><code>LayeredStore<S></code> is a generic aggregation wrapper over <code>Vec<S></code>. It propagates three traits from <code>obicompactvec::traits</code> up the hierarchy via blanket impls:</p>
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<div class="highlight"><pre><span></span><code><span class="k">pub</span><span class="w"> </span><span class="k">struct</span><span class="w"> </span><span class="nc">LayeredStore</span><span class="o"><</span><span class="n">S</span><span class="o">></span><span class="p">(</span><span class="k">pub</span><span class="w"> </span><span class="nb">Vec</span><span class="o"><</span><span class="n">S</span><span class="o">></span><span class="p">);</span>
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