Eric Coissac
5c1584967f
The command now supports reopening existing indexes instead of failing when the output file exists. Control flow branches between opening an existing index and constructing a new one, moving configuration setup exclusively to the creation path. Directory existence is enforced upfront with proper I/O error propagation. The --force flag retains its original semantics by removing the target directory before proceeding with a fresh build.
1800 lines
36 KiB
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1800 lines
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Chunk reader
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Construction pipeline
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obipipeline library
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On-disk storage
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MPHF selection
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Unitig evidence encoding
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Evidence elimination (discussion)
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obikindex layer tier
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PersistentCompactIntVec
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<h1 id="obitaxonomy-taxonomy-concept-paths"><code>obitaxonomy</code> — taxonomy concept paths</h1>
|
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<p><code>obitaxonomy</code> is a dependency-free crate that defines a typed representation
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of hierarchical concept paths (taxonomic or otherwise) stored in genome metadata.</p>
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<hr />
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<h2 id="concept-path-syntax">Concept path syntax</h2>
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<p>A concept path is stored as a metadata value with the prefix <code>taxonomy:/</code>:</p>
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<div class="highlight"><pre><span></span><code>taxonomy:/enterobacteriaceae@family/Escherichia@genus/Escherichia coli@species
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</code></pre></div>
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<p>Structure:</p>
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<ul>
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<li>The <code>taxonomy:/</code> prefix is the type discriminator. Any metadata value starting
|
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with it is parsed as a <code>TaxPath</code>; all others remain plain strings.</li>
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<li>The remainder is one or more <code>/</code>-separated segments.</li>
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<li>Each segment is <code>name</code> or <code>name@rank</code>, where <code>rank</code> is a label for the
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taxonomic level (e.g. <code>family</code>, <code>genus</code>, <code>species</code>).</li>
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<li>Rank annotations are <strong>optional per segment</strong> and can be mixed freely.</li>
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<li>Spaces are allowed in both names and ranks.</li>
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</ul>
|
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<h3 id="reserved-character">Reserved character</h3>
|
|
<p><code>@</code> is reserved throughout the taxonomy system and may <strong>not</strong> appear in:</p>
|
|
<table>
|
|
<thead>
|
|
<tr>
|
|
<th>Context</th>
|
|
<th>Constraint</th>
|
|
</tr>
|
|
</thead>
|
|
<tbody>
|
|
<tr>
|
|
<td>Segment name</td>
|
|
<td>forbidden</td>
|
|
</tr>
|
|
<tr>
|
|
<td>Rank/class label</td>
|
|
<td>forbidden</td>
|
|
</tr>
|
|
<tr>
|
|
<td>Metadata key names</td>
|
|
<td>forbidden (used as <code>key@rank</code> in predicate syntax)</td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
<p><code>@</code> is freely allowed in plain-text metadata values (non-taxonomy).</p>
|
|
<h3 id="parse-errors">Parse errors</h3>
|
|
<table>
|
|
<thead>
|
|
<tr>
|
|
<th>Condition</th>
|
|
<th>Error</th>
|
|
</tr>
|
|
</thead>
|
|
<tbody>
|
|
<tr>
|
|
<td>Value does not start with <code>taxonomy:/</code></td>
|
|
<td><code>MissingPrefix</code></td>
|
|
</tr>
|
|
<tr>
|
|
<td>No segments after the prefix</td>
|
|
<td><code>EmptyPath</code></td>
|
|
</tr>
|
|
<tr>
|
|
<td>Segment with empty name (consecutive <code>/</code>)</td>
|
|
<td><code>EmptySegmentName</code></td>
|
|
</tr>
|
|
<tr>
|
|
<td>Segment with trailing <code>@</code> and no rank (<code>name@</code>)</td>
|
|
<td><code>EmptyRankName</code></td>
|
|
</tr>
|
|
<tr>
|
|
<td>Segment with more than one <code>@</code></td>
|
|
<td><code>AmbiguousRank</code></td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
<hr />
|
|
<h2 id="public-api">Public API</h2>
|
|
<h3 id="taxsegment"><code>TaxSegment</code></h3>
|
|
<p>A single node: a name and an optional rank.</p>
|
|
<div class="highlight"><pre><span></span><code><span class="n">seg</span><span class="p">.</span><span class="n">name</span><span class="p">()</span><span class="w"> </span><span class="c1">// &str</span>
|
|
<span class="n">seg</span><span class="p">.</span><span class="n">rank</span><span class="p">()</span><span class="w"> </span><span class="c1">// Option<&str></span>
|
|
<span class="n">seg</span><span class="p">.</span><span class="n">to_string</span><span class="p">()</span><span class="w"> </span><span class="c1">// "name" or "name@rank"</span>
|
|
<span class="n">TaxSegment</span><span class="p">::</span><span class="n">parse</span><span class="p">(</span><span class="n">s</span><span class="p">)</span><span class="w"> </span><span class="c1">// Result<TaxSegment, TaxError></span>
|
|
</code></pre></div>
|
|
<h3 id="taxpath"><code>TaxPath</code></h3>
|
|
<div class="highlight"><pre><span></span><code><span class="n">TaxPath</span><span class="p">::</span><span class="n">parse</span><span class="p">(</span><span class="n">s</span><span class="p">)</span><span class="w"> </span><span class="c1">// Result<TaxPath, TaxError></span>
|
|
<span class="n">path</span><span class="p">.</span><span class="n">segments</span><span class="p">()</span><span class="w"> </span><span class="c1">// &[TaxSegment]</span>
|
|
<span class="n">path</span><span class="p">.</span><span class="n">depth</span><span class="p">()</span><span class="w"> </span><span class="c1">// usize — number of segments</span>
|
|
<span class="n">path</span><span class="p">.</span><span class="n">is_ancestor_of</span><span class="p">(</span><span class="o">&</span><span class="n">other</span><span class="p">)</span><span class="w"> </span><span class="c1">// bool — prefix match by name, ranks ignored</span>
|
|
<span class="n">path</span><span class="p">.</span><span class="n">name_at_rank</span><span class="p">(</span><span class="s">"genus"</span><span class="p">)</span><span class="w"> </span><span class="c1">// Option<&str></span>
|
|
<span class="n">path</span><span class="p">.</span><span class="n">to_string</span><span class="p">()</span><span class="w"> </span><span class="c1">// reconstructs "taxonomy:/…"</span>
|
|
</code></pre></div>
|
|
<p><code>is_ancestor_of</code> compares segment <strong>names</strong> only — rank annotations are
|
|
informational and do not affect the ancestry relation.</p>
|
|
<div class="highlight"><pre><span></span><code><span class="kd">let</span><span class="w"> </span><span class="n">a</span><span class="p">:</span><span class="w"> </span><span class="nc">TaxPath</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s">"taxonomy:/Enterobacteriaceae@family/Escherichia@genus"</span><span class="p">.</span><span class="n">parse</span><span class="p">()</span><span class="o">?</span><span class="p">;</span>
|
|
<span class="kd">let</span><span class="w"> </span><span class="n">b</span><span class="p">:</span><span class="w"> </span><span class="nc">TaxPath</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s">"taxonomy:/Enterobacteriaceae@family/Escherichia@genus/Escherichia coli@species"</span><span class="p">.</span><span class="n">parse</span><span class="p">()</span><span class="o">?</span><span class="p">;</span>
|
|
|
|
<span class="fm">assert!</span><span class="p">(</span><span class="n">a</span><span class="p">.</span><span class="n">is_ancestor_of</span><span class="p">(</span><span class="o">&</span><span class="n">b</span><span class="p">));</span><span class="w"> </span><span class="c1">// true</span>
|
|
<span class="fm">assert!</span><span class="p">(</span><span class="n">b</span><span class="p">.</span><span class="n">is_ancestor_of</span><span class="p">(</span><span class="o">&</span><span class="n">a</span><span class="p">));</span><span class="w"> </span><span class="c1">// false</span>
|
|
<span class="fm">assert!</span><span class="p">(</span><span class="n">a</span><span class="p">.</span><span class="n">is_ancestor_of</span><span class="p">(</span><span class="o">&</span><span class="n">a</span><span class="p">));</span><span class="w"> </span><span class="c1">// true (equal ⇒ ancestor)</span>
|
|
|
|
<span class="fm">assert_eq!</span><span class="p">(</span><span class="n">b</span><span class="p">.</span><span class="n">name_at_rank</span><span class="p">(</span><span class="s">"species"</span><span class="p">),</span><span class="w"> </span><span class="nb">Some</span><span class="p">(</span><span class="s">"Escherichia coli"</span><span class="p">));</span>
|
|
<span class="fm">assert_eq!</span><span class="p">(</span><span class="n">b</span><span class="p">.</span><span class="n">name_at_rank</span><span class="p">(</span><span class="s">"genus"</span><span class="p">),</span><span class="w"> </span><span class="nb">Some</span><span class="p">(</span><span class="s">"Escherichia"</span><span class="p">));</span>
|
|
<span class="fm">assert_eq!</span><span class="p">(</span><span class="n">b</span><span class="p">.</span><span class="n">name_at_rank</span><span class="p">(</span><span class="s">"order"</span><span class="p">),</span><span class="w"> </span><span class="nb">None</span><span class="p">);</span>
|
|
</code></pre></div>
|
|
<hr />
|
|
<h2 id="integration-with-genomeinfo">Integration with <code>GenomeInfo</code></h2>
|
|
<p>At index load time, every metadata value is inspected once:</p>
|
|
<ul>
|
|
<li>Starts with <code>taxonomy:/</code> → parsed into <code>TaxPath</code>, stored in <code>genome.taxonomy</code>.</li>
|
|
<li>Otherwise → kept as-is in <code>genome.meta</code>.</li>
|
|
</ul>
|
|
<div class="highlight"><pre><span></span><code><span class="k">struct</span><span class="w"> </span><span class="nc">GenomeInfo</span><span class="w"> </span><span class="p">{</span>
|
|
<span class="w"> </span><span class="n">label</span><span class="p">:</span><span class="w"> </span><span class="nb">String</span><span class="p">,</span>
|
|
<span class="w"> </span><span class="n">meta</span><span class="p">:</span><span class="w"> </span><span class="nc">HashMap</span><span class="o"><</span><span class="nb">String</span><span class="p">,</span><span class="w"> </span><span class="nb">String</span><span class="o">></span><span class="p">,</span><span class="w"> </span><span class="c1">// plain text metadata</span>
|
|
<span class="w"> </span><span class="n">taxonomy</span><span class="p">:</span><span class="w"> </span><span class="nc">HashMap</span><span class="o"><</span><span class="nb">String</span><span class="p">,</span><span class="w"> </span><span class="n">TaxPath</span><span class="o">></span><span class="p">,</span><span class="w"> </span><span class="c1">// parsed taxonomy metadata</span>
|
|
<span class="p">}</span>
|
|
</code></pre></div>
|
|
<p>The raw string is not duplicated. <code>TaxPath::to_string()</code> reconstructs the
|
|
original value losslessly for serialisation.</p>
|
|
<hr />
|
|
<h2 id="predicate-operators-in-filter-select">Predicate operators (in <code>filter</code> / <code>select</code>)</h2>
|
|
<p>Path predicates use the <code>~</code> / <code>!~</code> operators. The <strong>stored value</strong> always starts
|
|
with <code>/</code> (rooted path); the <strong>query pattern</strong> does not need to.</p>
|
|
<h3 id="path-pattern-syntax">Path pattern syntax</h3>
|
|
<table>
|
|
<thead>
|
|
<tr>
|
|
<th>Pattern</th>
|
|
<th>Semantics</th>
|
|
</tr>
|
|
</thead>
|
|
<tbody>
|
|
<tr>
|
|
<td><code>A/B</code></td>
|
|
<td>contiguous sub-path A then B, anywhere in the value</td>
|
|
</tr>
|
|
<tr>
|
|
<td><code>/A/B</code></td>
|
|
<td>value starts with A then B (start-anchored)</td>
|
|
</tr>
|
|
<tr>
|
|
<td><code>A/B$</code></td>
|
|
<td>value ends with A then B (end-anchored)</td>
|
|
</tr>
|
|
<tr>
|
|
<td><code>/A/B$</code></td>
|
|
<td>value is exactly A then B (fully anchored)</td>
|
|
</tr>
|
|
<tr>
|
|
<td><code>A@x/B</code></td>
|
|
<td>A with class <code>x</code> followed by B with any class</td>
|
|
</tr>
|
|
<tr>
|
|
<td><code>A@x/B@y</code></td>
|
|
<td>A with class <code>x</code> followed by B with class <code>y</code></td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
<p>A segment pattern without <code>@</code> matches the segment name regardless of its stored class.</p>
|
|
<h3 id="rank-aware-queries">Rank-aware queries</h3>
|
|
<div class="highlight"><pre><span></span><code>key@rank=value
|
|
</code></pre></div>
|
|
<table>
|
|
<thead>
|
|
<tr>
|
|
<th>Predicate form</th>
|
|
<th>Semantics</th>
|
|
</tr>
|
|
</thead>
|
|
<tbody>
|
|
<tr>
|
|
<td><code>key@rank=value</code></td>
|
|
<td>genome's <code>key</code> has <code>value</code> at rank <code>rank</code></td>
|
|
</tr>
|
|
<tr>
|
|
<td><code>key@rank!=value</code></td>
|
|
<td>does not</td>
|
|
</tr>
|
|
<tr>
|
|
<td><code>key@rank=v1\|v2</code></td>
|
|
<td>value at <code>rank</code> is <code>v1</code> or <code>v2</code></td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
<p><code>~</code> combined with <code>@rank</code> on the key (e.g. <code>key@genus~pattern</code>) is not defined
|
|
and is rejected at parse time.</p>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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