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add some doc about optimisation for query

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Eric Coissac
2026-08-20 13:59:12 +02:00
parent 89ea077456
commit a4eb20e67e
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DevDoc/implementation/benchmark_query_testing/index.html
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<li class="md-nav__item">
<a href="../benchmark_query_testing/" class="md-nav__link">
<span class="md-ellipsis">
Benchmark: query-path testing
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</a>
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</span>
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Benchmark: query-path testing
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Benchmark: query-path testing
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<li class="md-nav__item">
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Benchmark: query-path testing
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<li class="md-nav__item">
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Benchmark: query-path testing
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<li class="md-nav__item">
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Benchmark: query-path testing
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<li class="md-nav__item">
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Benchmark: query-path testing
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<li class="md-nav__item">
<a href="../benchmark_query_testing/" class="md-nav__link">
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Benchmark: query-path testing
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<li class="md-nav__item">
<a href="../benchmark_query_testing/" class="md-nav__link">
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Benchmark: query-path testing
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<li class="md-nav__item">
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Benchmark: query-path testing
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<li class="md-nav__item">
<a href="../benchmark_query_testing/" class="md-nav__link">
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Benchmark: query-path testing
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<li class="md-nav__item">
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Benchmark: query-path testing
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</span>
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</code></pre></div>
<hr/>
<h2 id="matrix-types">Matrix types</h2>
<p>Four matrix types, two encodings × two formats:</p>
<p>Both matrix types are enums behind a transparent API — the caller never matches on the variant. <code>PersistentCompactIntMatrix</code> has two variants (<code>Columnar</code>, <code>Packed</code>). <code>PersistentBitMatrix</code> has four:</p>
<table>
<thead>
<tr>
<th></th>
<th>Columnar format</th>
<th>Packed format</th>
<th>Variant</th>
<th>Storage</th>
<th>When</th>
</tr>
</thead>
<tbody>
<tr>
<td><strong>Bit</strong></td>
<td><code>PersistentBitMatrix</code> (Columnar variant)</td>
<td><code>PersistentBitMatrix</code> (Packed variant)</td>
<td><code>Columnar</code></td>
<td>one <code>.pbiv</code>/<code>.pciv</code> file per column + <code>meta.json</code></td>
<td>build-time default (<code>*Builder::new</code>)</td>
</tr>
<tr>
<td><strong>Int</strong></td>
<td><code>PersistentCompactIntMatrix</code> (Columnar variant)</td>
<td><code>PersistentCompactIntMatrix</code> (Packed variant)</td>
<td><code>Packed</code></td>
<td>single <code>matrix.pbmx</code> mmap file</td>
<td>query-optimised, produced by <code>pack_bit_matrix</code>/<code>pack_compact_int_matrix</code></td>
</tr>
<tr>
<td><code>Sparse</code> (bit only)</td>
<td><code>sparse_meta.json</code> + PFIV/Elias-Fano component files, row-major</td>
<td><code>pack --sparse</code>; see <a href="../../architecture/siblings/">siblings.md</a> for the sparse-vs-dense access-pattern trade-off</td>
</tr>
<tr>
<td><code>Implicit</code> (bit only)</td>
<td>no file at all</td>
<td>mono-genome presence layers — <code>n_cols</code> is always reported as <code>1</code>, every value is <code>true</code></td>
</tr>
</tbody>
</table>
<p>Both matrix types are enums (<code>Columnar</code> / <code>Packed</code> / <code>Implicit</code> for bit) behind a transparent API. <code>col_view(c)</code> returns the appropriate view directly:</p>
<p><code>PersistentBitMatrix::open(layer_dir)</code> auto-detects the variant, in order: <code>matrix.pbmx</code> → Packed, <code>presence/meta.json</code> → Columnar, <code>presence/sparse_meta.json</code> → Sparse, <code>layer_meta.json</code> (no presence dir at all) → Implicit. <code>col_view</code>/<code>col</code>/<code>sub_matrix</code> panic on <code>Sparse</code>/<code>Implicit</code> where the operation has no direct-slice equivalent (Sparse is k-mer-major, not column-major; Implicit has no backing storage) — callers needing per-column data on those variants go through <code>row</code>/<code>fill_row</code>.</p>
<p><code>col_view(c)</code> returns the appropriate view directly:</p>
<div class="highlight"><pre><span></span><code><span class="c1">// PersistentBitMatrix</span>
<span class="k">pub</span><span class="w"> </span><span class="k">fn</span><span class="w"> </span><span class="nf">col_view</span><span class="p">(</span><span class="o">&amp;</span><span class="bp">self</span><span class="p">,</span><span class="w"> </span><span class="n">c</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">-&gt;</span><span class="w"> </span><span class="nc">BitSliceView</span><span class="o">&lt;'</span><span class="nb">_</span><span class="o">&gt;</span>
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<li class="md-nav__item">
<a href="../benchmark_query_testing/" class="md-nav__link">
<span class="md-ellipsis">
Benchmark: query-path testing
</span>
</a>
</li>
</ul>
</nav>
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</ul>
</nav>
</li>
<li class="md-nav__item">
<a href="#layerd-raw-mapping-iteration-and-batch-access" class="md-nav__link">
<span class="md-ellipsis">
Layer\&lt;D> — raw mapping, iteration, and batch access
</span>
</a>
<nav class="md-nav" aria-label="Layer\&lt;D&gt; — raw mapping, iteration, and batch access">
<ul class="md-nav__list">
<li class="md-nav__item">
<a href="#raw-kmer-slot-mapping" class="md-nav__link">
<span class="md-ellipsis">
Raw kmer → slot mapping
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#kmer-iteration" class="md-nav__link">
<span class="md-ellipsis">
Kmer iteration
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#batch-lookup-on-payload-vectorsviews" class="md-nav__link">
<span class="md-ellipsis">
Batch lookup on payload vectors/views
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#sub_matrix-fill_sub_matrix" class="md-nav__link">
<span class="md-ellipsis">
sub_matrix / fill_sub_matrix
</span>
</a>
</li>
</ul>
</nav>
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@@ -1263,6 +1324,34 @@
<li class="md-nav__item">
<a href="../benchmark_query_testing/" class="md-nav__link">
<span class="md-ellipsis">
Benchmark: query-path testing
</span>
</a>
</li>
</ul>
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@@ -1638,6 +1727,67 @@
</ul>
</nav>
</li>
<li class="md-nav__item">
<a href="#layerd-raw-mapping-iteration-and-batch-access" class="md-nav__link">
<span class="md-ellipsis">
Layer\&lt;D> — raw mapping, iteration, and batch access
</span>
</a>
<nav class="md-nav" aria-label="Layer\&lt;D&gt; — raw mapping, iteration, and batch access">
<ul class="md-nav__list">
<li class="md-nav__item">
<a href="#raw-kmer-slot-mapping" class="md-nav__link">
<span class="md-ellipsis">
Raw kmer → slot mapping
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#kmer-iteration" class="md-nav__link">
<span class="md-ellipsis">
Kmer iteration
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#batch-lookup-on-payload-vectorsviews" class="md-nav__link">
<span class="md-ellipsis">
Batch lookup on payload vectors/views
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#sub_matrix-fill_sub_matrix" class="md-nav__link">
<span class="md-ellipsis">
sub_matrix / fill_sub_matrix
</span>
</a>
</li>
</ul>
</nav>
</li>
<li class="md-nav__item">
@@ -2000,6 +2150,38 @@
</code></pre></div>
<p>Mode 3 (<code>PersistentBitMatrix</code>) has no <code>push_layer</code> on <code>LayeredMap</code>; callers build directly via <code>Layer&lt;PersistentBitMatrix&gt;::build_presence</code>.</p>
<hr />
<h2 id="layerd-raw-mapping-iteration-and-batch-access">Layer\&lt;D&gt; — raw mapping, iteration, and batch access</h2>
<p>Beyond <code>query</code>/<code>find</code> (membership-checked), <code>Layer&lt;D&gt;</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>
<h3 id="raw-kmer-slot-mapping">Raw kmer → slot mapping</h3>
<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">&amp;</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">-&gt;</span><span class="w"> </span><span class="kt">usize</span>
<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">&amp;</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">&amp;</span><span class="p">[</span><span class="n">CanonicalKmer</span><span class="p">])</span><span class="w"> </span><span class="p">-&gt;</span><span class="w"> </span><span class="nb">Vec</span><span class="o">&lt;</span><span class="kt">usize</span><span class="o">&gt;</span>
</code></pre></div>
<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>
<h3 id="kmer-iteration">Kmer iteration</h3>
<p>Four iterators, all built from <code>unitigs.bin</code> (physical layout order, <strong>not</strong> correlated with MPHF slot numbers):</p>
<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">&amp;</span><span class="bp">self</span><span class="p">)</span><span class="w"> </span><span class="p">-&gt;</span><span class="w"> </span><span class="nc">KmerIter</span><span class="o">&lt;&#39;</span><span class="nb">_</span><span class="o">&gt;</span>
<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">&amp;</span><span class="bp">self</span><span class="p">)</span><span class="w"> </span><span class="p">-&gt;</span><span class="w"> </span><span class="nc">Enumerate</span><span class="o">&lt;</span><span class="n">KmerIter</span><span class="o">&lt;&#39;</span><span class="nb">_</span><span class="o">&gt;&gt;</span><span class="w"> </span><span class="c1">// (order_index, kmer)</span>
<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">&amp;</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">-&gt;</span><span class="w"> </span><span class="nc">KmerBatchIter</span><span class="o">&lt;&#39;</span><span class="nb">_</span><span class="o">&gt;</span><span class="w"> </span><span class="c1">// Vec&lt;CanonicalKmer&gt; of size ≤ n</span>
<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">&amp;</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">-&gt;</span><span class="w"> </span><span class="nc">impl</span><span class="w"> </span><span class="nb">Iterator</span><span class="o">&lt;</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">&lt;</span><span class="n">CanonicalKmer</span><span class="o">&gt;</span><span class="p">)</span><span class="o">&gt;</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">&#39;</span><span class="nb">static</span>
</code></pre></div>
<p><code>KmerIter</code>/<code>KmerBatchIter</code> own a clone of the underlying <code>Arc&lt;UnitigFileReader&gt;</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>
<h3 id="batch-lookup-on-payload-vectorsviews">Batch lookup on payload vectors/views</h3>
<p><code>PersistentCompactIntVec</code>, <code>PersistentBitVec</code>, <code>IntSliceView</code>, <code>BitSliceView</code> all expose:</p>
<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">&amp;</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">&amp;</span><span class="p">[</span><span class="kt">usize</span><span class="p">])</span><span class="w"> </span><span class="p">-&gt;</span><span class="w"> </span><span class="nb">Vec</span><span class="o">&lt;</span><span class="n">T</span><span class="o">&gt;</span>
<span class="k">fn</span><span class="w"> </span><span class="nf">fill_batch</span><span class="p">(</span><span class="o">&amp;</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">&amp;</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">&amp;</span><span class="nc">mut</span><span class="w"> </span><span class="p">[</span><span class="n">T</span><span class="p">])</span>
</code></pre></div>
<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>
<h3 id="sub_matrix-fill_sub_matrix">sub_matrix / fill_sub_matrix</h3>
<div class="highlight"><pre><span></span><code><span class="c1">// Layer&lt;PersistentCompactIntMatrix&gt;</span>
<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">&amp;</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">&amp;</span><span class="p">[</span><span class="kt">usize</span><span class="p">])</span><span class="w"> </span><span class="p">-&gt;</span><span class="w"> </span><span class="nb">Vec</span><span class="o">&lt;</span><span class="nb">Vec</span><span class="o">&lt;</span><span class="kt">u32</span><span class="o">&gt;&gt;</span><span class="w"> </span><span class="c1">// column-first</span>
<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">&amp;</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">&amp;</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">&amp;</span><span class="nc">mut</span><span class="w"> </span><span class="p">[</span><span class="nb">Vec</span><span class="o">&lt;</span><span class="kt">u32</span><span class="o">&gt;</span><span class="p">])</span>
<span class="c1">// Layer&lt;PersistentBitMatrix&gt; (and any D: BinaryMatrix, e.g. PersistentSparseBitMatrix)</span>
<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">&amp;</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">&amp;</span><span class="p">[</span><span class="kt">usize</span><span class="p">])</span><span class="w"> </span><span class="p">-&gt;</span><span class="w"> </span><span class="nb">Vec</span><span class="o">&lt;</span><span class="nb">Vec</span><span class="o">&lt;</span><span class="kt">bool</span><span class="o">&gt;&gt;</span>
<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">&amp;</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">&amp;</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">&amp;</span><span class="nc">mut</span><span class="w"> </span><span class="p">[</span><span class="nb">Vec</span><span class="o">&lt;</span><span class="kt">bool</span><span class="o">&gt;</span><span class="p">])</span>
</code></pre></div>
<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>
<hr />
<h2 id="layeredstores-and-aggregation-traits">LayeredStore\&lt;S&gt; and aggregation traits</h2>
<p><code>LayeredStore&lt;S&gt;</code> is a generic aggregation wrapper over <code>Vec&lt;S&gt;</code>. It propagates three traits from <code>obicompactvec::traits</code> up the hierarchy via blanket impls:</p>
<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">&lt;</span><span class="n">S</span><span class="o">&gt;</span><span class="p">(</span><span class="k">pub</span><span class="w"> </span><span class="nb">Vec</span><span class="o">&lt;</span><span class="n">S</span><span class="o">&gt;</span><span class="p">);</span>
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