Eric Coissac
f36b095ce2
Formalize the two-phase MPHF indexing architecture and update Phase 6 to use `evidence.bin` for direct kmer extraction. Simplify the evidence and unitig storage layouts to flat packed formats enabling O(1) random access. Introduce aggregation traits (`ColumnWeights`, `CountPartials`, `BitPartials`) to support additive distance metric decomposition across partitions. Narrow the documented scope from metagenomic to individual genome datasets, and replace speculative open questions with concrete implementation specifications.
1226 lines
39 KiB
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1226 lines
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obipipeline library
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MPHF selection
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Unitig evidence encoding
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Unitig evidence encoding
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Role of unitigs in the index
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Strategy A — global nucleotide offset
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Strategy B — (unitig_id, rank within unitig)
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Savings from u8 length fields
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Empirical observation: m_u is set by De Bruijn graph topology, not partition count
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Per-partition compaction ratio (sk_symbols / u_symbols)
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Evidence file layout (strategy B — implemented)
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Unitig file layout
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Decoding a kmer from slot s
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Field widths in practice
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Non-determinism of the unitig decomposition
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Consequence for MPHF construction
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|
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Open questions
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obilayeredmap crate
|
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|
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|
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PersistentCompactIntVec
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<span class="md-ellipsis">
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|
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PersistentBitVec
|
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|
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</span>
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Architecture
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Sequences
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Kmer index
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Role of unitigs in the index
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Two encoding strategies
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Strategy A — global nucleotide offset
|
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Strategy B — (unitig_id, rank within unitig)
|
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Bit-cost analysis
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Empirical bound on unitig length
|
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Split strategy for long unitigs
|
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|
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Savings from u8 length fields
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Partition-size tradeoff
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|
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|
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Empirical observation: m_u is set by De Bruijn graph topology, not partition count
|
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Per-partition compaction ratio (sk_symbols / u_symbols)
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Evidence file layout (strategy B — implemented)
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Unitig file layout
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Decoding a kmer from slot s
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Field widths in practice
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<li class="md-nav__item">
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Forward vs reverse complement
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Non-determinism of the unitig decomposition
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Consequence for MPHF construction
|
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Open questions
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<div class="md-content" data-md-component="content">
|
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<article class="md-content__inner md-typeset">
|
||
<h1 id="unitig-based-mphf-evidence-encoding">Unitig-based MPHF evidence encoding</h1>
|
||
<h2 id="role-of-unitigs-in-the-index">Role of unitigs in the index</h2>
|
||
<p>The MPHF maps each canonical kmer to an integer slot, but provides no way to reconstruct the kmer from its slot. A downstream operation (query, set operation) that receives a slot index and needs the kmer sequence must be able to retrieve it. The <strong>evidence file</strong> serves this purpose: it stores the kmer sequences in compact form and provides, for each MPHF slot, a pointer to where the corresponding kmer can be decoded.</p>
|
||
<p>Unitigs are the natural compact representation: a run of L nucleotides encodes L − k + 1 consecutive canonical kmers. The entire kmer set of a partition can be reconstructed from its unitig FASTA file.</p>
|
||
<hr/>
|
||
<h2 id="two-encoding-strategies">Two encoding strategies</h2>
|
||
<h3 id="strategy-a-global-nucleotide-offset">Strategy A — global nucleotide offset</h3>
|
||
<p>Each MPHF slot stores a single integer: the byte offset of the kmer's first nucleotide within a packed 2-bit nucleotide array that concatenates all unitigs.</p>
|
||
<div class="highlight"><pre><span></span><code>evidence[slot] = global_offset (bits: ⌈log₂ N_nuc⌉)
|
||
</code></pre></div>
|
||
<p>where <code>N_nuc</code> is the total number of nucleotides across all unitigs in the partition.</p>
|
||
<p>Decoding: read k nucleotides starting at <code>global_offset</code>.</p>
|
||
<h3 id="strategy-b-unitig_id-rank-within-unitig">Strategy B — (unitig_id, rank within unitig)</h3>
|
||
<p>Each MPHF slot stores a pair:</p>
|
||
<div class="highlight"><pre><span></span><code>evidence[slot] = (unitig_id, rank)
|
||
</code></pre></div>
|
||
<ul>
|
||
<li><code>unitig_id</code> : index of the unitig in the partition (0-based)</li>
|
||
<li><code>rank</code> : kmer index within the unitig (0 ≤ rank < n_kmers); kmer i starts at nucleotide i, so the nucleotide offset is identical numerically but the kmer-unit interpretation is the natural one</li>
|
||
</ul>
|
||
<p>Decoding: look up the unitig at <code>unitig_id</code>, then read k nucleotides starting at <code>rank</code>.</p>
|
||
<hr/>
|
||
<h2 id="bit-cost-analysis">Bit-cost analysis</h2>
|
||
<p>Define for a partition of P kmers with average kmers-per-unitig m:</p>
|
||
<ul>
|
||
<li>total nucleotides: <span class="arithmatex">\(N_{nuc} = P \cdot \left(1 + \dfrac{k-1}{m}\right)\)</span></li>
|
||
<li>number of unitigs: <span class="arithmatex">\(U = P / m\)</span></li>
|
||
</ul>
|
||
<p><strong>Strategy A</strong></p>
|
||
<div class="arithmatex">\[
|
||
b_A = \left\lceil \log_2 N_{nuc} \right\rceil = \left\lceil \log_2 P + \log_2\!\left(1 + \frac{k-1}{m}\right) \right\rceil
|
||
\]</div>
|
||
<p><strong>Strategy B</strong></p>
|
||
<div class="arithmatex">\[
|
||
b_B = \left\lceil \log_2 U \right\rceil + \left\lceil \log_2 L_{max} \right\rceil
|
||
\]</div>
|
||
<p>where <span class="arithmatex">\(L_{max}\)</span> is the maximum unitig length (in nucleotides). In practice <span class="arithmatex">\(L_{max} \ll P\)</span>, so the rank field is much cheaper than the full global offset. If unitig lengths are bounded (e.g. by partition structure), the rank field width is a small constant independent of P.</p>
|
||
<h3 id="empirical-bound-on-unitig-length">Empirical bound on unitig length</h3>
|
||
<p>Lengths and ranks are expressed in <strong>kmer units</strong> (not nucleotides): the nucleotide length is <code>n_kmers + k − 1</code>, so storing <code>n_kmers</code> instead of <code>seq_length</code> saves k−1 = 30 units of headroom in the same field width.</p>
|
||
<p>Consequence for <code>u8</code> capacity:</p>
|
||
<table>
|
||
<thead>
|
||
<tr>
|
||
<th>unit</th>
|
||
<th>max representable</th>
|
||
<th>max nucleotides</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr>
|
||
<td>nucleotides</td>
|
||
<td>255 nuc</td>
|
||
<td>225 kmers</td>
|
||
</tr>
|
||
<tr>
|
||
<td><strong>kmers</strong></td>
|
||
<td><strong>255 kmers</strong></td>
|
||
<td><strong>285 nuc</strong></td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
<p><strong>Structural maximum from superkmer construction.</strong> For k=31 and m=11, the maximum number of consecutive kmers sharing the same minimiser is k − m + 1 = <strong>21 kmers</strong> (the minimiser traverses from position k−m to 0 as the window slides). A unitig that is a single full superkmer therefore has exactly 21 kmers. This is confirmed by a bimodal distribution in empirical data: a sharp peak at 21 kmers appears in all partitions, including the anomalous partition 145. The observed maximum is ~46 kmers (unitigs spanning more than one superkmer), well within u8 range.</p>
|
||
<p>On <em>Betula nana</em> (k=31, 256 partitions), m_u ≈ 37.9 kmers/unitig on average. The <code>rank</code> field (kmer index within the unitig) fits in a <code>u8</code> as long as no unitig exceeds 255 kmers — guaranteed by the split strategy below and amply satisfied by empirical maximums (~46 kmers observed).</p>
|
||
<h3 id="split-strategy-for-long-unitigs">Split strategy for long unitigs</h3>
|
||
<p>For the rare cases where a unitig exceeds 255 kmers, the unitig is split into chunks of at most 255 kmers, with a <strong>k−1 nucleotide overlap</strong> at each junction — identical to the way super-kmers are delimited at partition boundaries. Each chunk is self-contained and independently decodable.</p>
|
||
<div class="highlight"><pre><span></span><code>original unitig: kmer_0 … kmer_254 | kmer_255 … kmer_N
|
||
↑ cut here
|
||
|
||
chunk 1: nucleotides 0 … 284 (255 kmers)
|
||
chunk 2: nucleotides 255 … N+k-1 (N-255+1 kmers)
|
||
shared: nucleotides 255 … 284 (k-1 = 30 nucleotides, stored in both)
|
||
</code></pre></div>
|
||
<p>Cost of one split: k−1 = 30 redundant nucleotides = 60 bits. This event is rare in practice (m_u ≈ 38 for <em>B. nana</em>, well below the 255-kmer cap). No kmer is lost: kmer i is in chunk 1 if i < 255, in chunk 2 (at rank i−255) otherwise.</p>
|
||
<h3 id="savings-from-u8-length-fields">Savings from u8 length fields</h3>
|
||
<p>Because all chunks are guaranteed ≤ 255 kmers, the per-chunk length array in the binary index is a flat <code>u8</code> array — 1 byte per chunk instead of 8 bytes (usize) or 4 bytes (u32). For a partition with 4 M unitigs:</p>
|
||
<table>
|
||
<thead>
|
||
<tr>
|
||
<th>length type</th>
|
||
<th>bytes/chunk</th>
|
||
<th>total (4 M chunks)</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr>
|
||
<td>usize (u64)</td>
|
||
<td>8</td>
|
||
<td>32 MB</td>
|
||
</tr>
|
||
<tr>
|
||
<td>u32</td>
|
||
<td>4</td>
|
||
<td>16 MB</td>
|
||
</tr>
|
||
<tr>
|
||
<td><strong>u8</strong></td>
|
||
<td><strong>1</strong></td>
|
||
<td><strong>4 MB</strong></td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
<p>Random access to chunk i is recovered at load time by a single prefix-sum pass over the u8 array, computing a u32/u64 offset array in O(n_chunks) time and O(n_chunks × 4) bytes — paid once at open time, cached for the lifetime of the partition handle.</p>
|
||
<p>Bit costs for <em>Betula nana</em> (k=31, 256 partitions, P ≈ 10.4 M, U ≈ 275 k, m_u ≈ 37.9):</p>
|
||
<table>
|
||
<thead>
|
||
<tr>
|
||
<th>field</th>
|
||
<th>strategy A</th>
|
||
<th>strategy B</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr>
|
||
<td>offset / id</td>
|
||
<td><span class="arithmatex">\(\lceil\log_2(P \cdot (1 + 30/m_u))\rceil = 25\)</span> bits</td>
|
||
<td><span class="arithmatex">\(\lceil\log_2(U)\rceil = 19\)</span> bits</td>
|
||
</tr>
|
||
<tr>
|
||
<td>rank</td>
|
||
<td>—</td>
|
||
<td>8 bits (u8, fixed)</td>
|
||
</tr>
|
||
<tr>
|
||
<td><strong>total</strong></td>
|
||
<td><strong>25 bits</strong></td>
|
||
<td><strong>27 bits</strong></td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
<p>Strategy A is 2 bits cheaper. Strategy B's main advantage is <strong>locality</strong>: decoding a kmer touches one unitig's cache lines rather than an arbitrary offset in a large flat array, and the <code>rank</code> field doubles as a direct index into the packed nucleotide sequence without pointer arithmetic.</p>
|
||
<hr/>
|
||
<h2 id="partition-size-tradeoff">Partition-size tradeoff</h2>
|
||
<p>The total bits/kmer for the index (sequence + evidence + MPHF) as a function of partition size is:</p>
|
||
<div class="arithmatex">\[
|
||
\text{total} = \underbrace{2\!\left(1 + \frac{k-1}{m}\right)}_{\text{sequence}} + \underbrace{\log_2 P + \log_2\!\left(1+\frac{k-1}{m}\right)}_{\text{evidence}} + \underbrace{c_{MPHF}}_{\approx 2\text{–}4}
|
||
\]</div>
|
||
<h3 id="empirical-observation-m_u-is-set-by-de-bruijn-graph-topology-not-partition-count">Empirical observation: m_u is set by De Bruijn graph topology, not partition count</h3>
|
||
<p>Measured on <em>Betula nana</em> (k=31, m=11), summing n_kmers and sequence counts across all partition files:</p>
|
||
<table>
|
||
<thead>
|
||
<tr>
|
||
<th>N partitions</th>
|
||
<th>m_sk</th>
|
||
<th>m_u</th>
|
||
<th>factor m_u/m_sk</th>
|
||
<th>nuc ratio (u/sk)</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr>
|
||
<td>1</td>
|
||
<td>12.13</td>
|
||
<td><strong>41.89</strong></td>
|
||
<td>3.45×</td>
|
||
<td>0.273</td>
|
||
</tr>
|
||
<tr>
|
||
<td>16</td>
|
||
<td>12.13</td>
|
||
<td><strong>38.19</strong></td>
|
||
<td>3.15×</td>
|
||
<td>0.376</td>
|
||
</tr>
|
||
<tr>
|
||
<td>256</td>
|
||
<td>12.13</td>
|
||
<td><strong>37.90</strong></td>
|
||
<td>3.12×</td>
|
||
<td>0.388</td>
|
||
</tr>
|
||
<tr>
|
||
<td>1 024</td>
|
||
<td>12.13</td>
|
||
<td><strong>37.89</strong></td>
|
||
<td>3.12×</td>
|
||
<td>0.389</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
<ul>
|
||
<li><code>m_sk</code> = avg kmers/super-kmer (invariant — same dataset regardless of partition scheme)</li>
|
||
<li><code>m_u</code> = avg kmers/unitig = total_n_kmers / total_unitigs, summed across all partitions</li>
|
||
<li><code>nuc ratio</code> = (u_symbols + 30·u_reads) / (sk_symbols + 30·sk_reads)</li>
|
||
</ul>
|
||
<p>X-axis in both charts: partition bits (0 = 1 partition, 10 = 1024 partitions) — each step doubles the partition count.</p>
|
||
<pre class="mermaid"><code>xychart-beta
|
||
title "m_u (avg kmers/unitig) vs partition bits — B. nana k=31"
|
||
x-axis "partition bits" 0 --> 10
|
||
y-axis "m_u" 37 --> 43
|
||
line [41.89, 40.78, 39.22, 38.52, 38.19, 38.03, 37.96, 37.92, 37.90, 37.89, 37.89]</code></pre>
|
||
<pre class="mermaid"><code>xychart-beta
|
||
title "Nucleotide storage: unitigs / super-kmers (%) vs partition bits — B. nana k=31"
|
||
x-axis "partition bits" 0 --> 10
|
||
y-axis "%" 25 --> 42
|
||
line [27.3, 29.7, 33.9, 36.3, 37.6, 38.3, 38.6, 38.7, 38.8, 38.9, 38.9]</code></pre>
|
||
<p>Key observations:</p>
|
||
<ol>
|
||
<li><strong>Partition boundaries have a small but non-zero effect on m_u.</strong> Going from 1 to 1024 partitions reduces m_u by 10% (41.9 → 37.9). Within the practical range 16–1024, the variation is under 1% — m_u is effectively constant.</li>
|
||
<li><strong>m_u is a property of the De Bruijn graph, not the partition scheme.</strong> The dominant factor is graph branching (heterozygosity, repeats, sequencing errors).</li>
|
||
<li><strong>Unitigs provide substantial compaction over super-kmers.</strong> At 256 partitions, unitigs cover the same unique kmers using 39% of the raw nucleotide content of super-kmers (3.1× compaction factor).</li>
|
||
</ol>
|
||
<h4 id="per-partition-compaction-ratio-sk_symbols-u_symbols">Per-partition compaction ratio (sk_symbols / u_symbols)</h4>
|
||
<p>The ratio measures how much super-kmer kmer-slots are "shared" across different super-kmer records: a ratio of 1.35 means each unique kmer (counted once in unitigs) appears in 1.35 super-kmer kmer-slots on average.</p>
|
||
<table>
|
||
<thead>
|
||
<tr>
|
||
<th>bits</th>
|
||
<th>N partitions</th>
|
||
<th>median ratio</th>
|
||
<th>min ratio</th>
|
||
<th>min partition</th>
|
||
<th>min u_reads</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr>
|
||
<td>6</td>
|
||
<td>64</td>
|
||
<td>1.355</td>
|
||
<td>1.073</td>
|
||
<td>—</td>
|
||
<td>4.5 M</td>
|
||
</tr>
|
||
<tr>
|
||
<td>7</td>
|
||
<td>128</td>
|
||
<td>1.352</td>
|
||
<td>1.037</td>
|
||
<td>—</td>
|
||
<td>4.1 M</td>
|
||
</tr>
|
||
<tr>
|
||
<td>8</td>
|
||
<td>256</td>
|
||
<td><strong>1.350</strong></td>
|
||
<td><strong>1.012</strong></td>
|
||
<td><strong>145</strong></td>
|
||
<td><strong>3.8 M</strong></td>
|
||
</tr>
|
||
<tr>
|
||
<td>9</td>
|
||
<td>512</td>
|
||
<td>1.350</td>
|
||
<td>0.998</td>
|
||
<td>145</td>
|
||
<td>3.6 M</td>
|
||
</tr>
|
||
<tr>
|
||
<td>10</td>
|
||
<td>1024</td>
|
||
<td>1.351</td>
|
||
<td>0.992</td>
|
||
<td>145</td>
|
||
<td>3.6 M</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
<p>The median stabilises at <strong>1.35</strong> from 64 partitions onward (stdev = 0.027 at 256 partitions). There is one persistent outlier: <strong>partition 145</strong> (at 256-partition resolution) is consistently anomalous across all partition depths — it contains 10–14× more super-kmers and unitigs than the average partition, with a ratio near 1.0, meaning the unitig representation provides almost no kmer deduplication. This is consistent with a highly repetitive or organellar region where the dominant minimiser belongs to a sequence that appears in many reads without forming long overlapping paths in the De Bruijn graph.</p>
|
||
<p>Per-partition parameters at 256 partitions (<em>B. nana</em>):</p>
|
||
<table>
|
||
<thead>
|
||
<tr>
|
||
<th>quantity</th>
|
||
<th>value</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr>
|
||
<td>P (unique kmers/partition, avg)</td>
|
||
<td>≈ 10.4 M</td>
|
||
</tr>
|
||
<tr>
|
||
<td>U (unitigs/partition, avg)</td>
|
||
<td>≈ 275 k</td>
|
||
</tr>
|
||
<tr>
|
||
<td>m_u</td>
|
||
<td>≈ 37.9</td>
|
||
</tr>
|
||
<tr>
|
||
<td>Strategy A bits/kmer</td>
|
||
<td>⌈log₂(P·(1+30/m_u))⌉ = 25</td>
|
||
</tr>
|
||
<tr>
|
||
<td>Strategy B bits/kmer</td>
|
||
<td>⌈log₂(U)⌉ + 8 = 27</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
<p>Consequence: <strong>the partition count should be as large as memory and parallelism allow.</strong> Each doubling saves 1 bit/kmer in evidence (log₂ P decreases by 1). The sequence term 2·(1 + 30/m_u) ≈ 3.6 bits/kmer is approximately constant.</p>
|
||
<p>Strategy B partially decouples evidence cost from P: <code>log₂(U) = log₂(P/m_u)</code> grows more slowly than <code>log₂(P)</code> by a fixed log₂(m_u) ≈ 5 bits. Strategy B's main benefit remains locality and bounded rank width, not asymptotic compression.</p>
|
||
<hr/>
|
||
<h2 id="implementation-notes">Implementation notes</h2>
|
||
<h3 id="evidence-file-layout-strategy-b-implemented">Evidence file layout (strategy B — implemented)</h3>
|
||
<p><code>evidence.bin</code> is a flat <code>[u32; n]</code> array with no header:</p>
|
||
<div class="highlight"><pre><span></span><code>evidence.bin: n × 4 bytes, little-endian
|
||
each u32: bits [31:7] = chunk_id (25 bits)
|
||
bits [6:0] = rank (7 bits)
|
||
</code></pre></div>
|
||
<p>File size = <code>n × 4</code> bytes exactly. Decoding a slot: <code>chunk_id = raw >> 7</code>, <code>rank = raw & 0x7F</code>.</p>
|
||
<p>The theoretical bit cost of strategy B (19 bits id + 8 bits rank = 27 bits) is not recovered: packing into aligned u32 costs 32 bits per slot. The u32 layout is chosen for simplicity and alignment — one word per slot, no bit-addressing arithmetic.</p>
|
||
<h3 id="unitig-file-layout">Unitig file layout</h3>
|
||
<p>Binary packed 2-bit nucleotide file (<code>unitigs.bin</code>) with a companion index (<code>unitigs.bin.idx</code>). The index stores: magic <code>UIDX</code>, <code>n_unitigs: u32</code>, <code>n_kmers: u64</code>, <code>seqls: [u8; n_unitigs]</code> (kmer count − 1 per chunk), and <code>packed_offsets: [u32; n_unitigs + 1]</code> (byte offsets into <code>unitigs.bin</code>, sentinel-terminated). This gives O(1) random access to any unitig and the total kmer count without scanning the sequence file.</p>
|
||
<h3 id="decoding-a-kmer-from-slot-s">Decoding a kmer from slot s</h3>
|
||
<div class="highlight"><pre><span></span><code>(chunk_id, rank) = evidence.decode(s) // u32 → (u25, u7)
|
||
kmer = unitigs.raw_kmer(chunk_id, rank) // 2-bit packed slice, k nucleotides
|
||
</code></pre></div>
|
||
<p>Two memory accesses: one into <code>evidence.bin</code>, one into <code>unitigs.bin</code>. The canonical kmer is the stored sequence (by construction — only canonical kmers are inserted into the De Bruijn graph).</p>
|
||
<h3 id="field-widths-in-practice">Field widths in practice</h3>
|
||
<p>Rank is stored in 7 bits (0–127). On <em>B. nana</em> (k=31, m=11), the observed maximum unitig length is ~46 kmers/chunk — well within the 127-kmer u7 capacity. The structural maximum from superkmer construction is k − m + 1 = 21 kmers per unitig; longer paths arise across multiple superkmers. u7 is sufficient.</p>
|
||
<p>chunk_id is stored in 25 bits (0–33 554 431). For <em>B. nana</em> at 256 partitions, avg U ≈ 275 k — well within the 25-bit capacity.</p>
|
||
<h3 id="forward-vs-reverse-complement">Forward vs reverse complement</h3>
|
||
<p>The De Bruijn graph stores only canonical kmers. The evidence encodes the canonical orientation. Callers that need the strand of the original kmer must compare the retrieved kmer with its revcomp at query time; this is a single 64-bit comparison.</p>
|
||
<hr/>
|
||
<h2 id="non-determinism-of-the-unitig-decomposition">Non-determinism of the unitig decomposition</h2>
|
||
<p>The unitig extraction is <strong>not deterministic</strong>: two runs on identical input can produce a different number of unitigs with different sequences, while covering exactly the same canonical k-mer set.</p>
|
||
<h3 id="source-of-non-determinism">Source of non-determinism</h3>
|
||
<p>The graph nodes are stored in a hash map whose iteration order depends on the hash seed (random per run with <code>ahash::RandomState::new()</code>). The <code>start_iter</code> first pass emits every node whose <code>can_extend_left</code> flag is false — which includes not only true dead-end nodes but also <strong>branch points</strong> (nodes with 2 or more left neighbours, for which <code>unique_neighbor</code> returns <code>None</code>).</p>
|
||
<p>When a branch point is encountered before its upstream neighbours, it claims the downstream chain and those neighbours later produce length-k degenerate unitigs. When upstream neighbours are encountered first, they extend through the branch point and consume it.</p>
|
||
<p><strong>Example</strong> — fork topology (k = 31):</p>
|
||
<div class="highlight"><pre><span></span><code>A → B ← C
|
||
↓
|
||
D
|
||
</code></pre></div>
|
||
<p>All four nodes are in the graph. B has two left neighbours (A and C), so <code>can_extend_left = false</code>; B also has one right neighbour D, so <code>can_extend_right = true</code>.</p>
|
||
<table>
|
||
<thead>
|
||
<tr>
|
||
<th>iteration order</th>
|
||
<th>unitigs produced</th>
|
||
<th>count</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr>
|
||
<td>A first, then B, C</td>
|
||
<td>ABD · C</td>
|
||
<td>2</td>
|
||
</tr>
|
||
<tr>
|
||
<td>B first, then A, C</td>
|
||
<td>BD · A · C</td>
|
||
<td>3</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
<p>Both tilings cover the same 4 canonical k-mers.</p>
|
||
<p>Pure cycles (all nodes have both extensions present) are unaffected by this: they are never emitted in the first pass and each cycle produces exactly one unitig regardless of which node the second pass starts from. Only the cycle cut point (and therefore the sequence content) varies.</p>
|
||
<h3 id="consequence-for-mphf-construction">Consequence for MPHF construction</h3>
|
||
<p>The MPHF is built from the <strong>k-mer set</strong>, not from the unitig sequences themselves. Because both tilings contain the same canonical k-mers, the resulting MPHF is identical. The non-determinism is benign for this use case.</p>
|
||
<hr/>
|
||
<h2 id="open-questions">Open questions</h2>
|
||
<ul>
|
||
<li><strong>Cross-partition evidence</strong>: for set operations spanning multiple partitions, strategy B allows unitig-level operations (e.g. mark entire unitigs as present/absent) rather than kmer-level, potentially reducing the operation cost by a factor of m_u.</li>
|
||
</ul>
|
||
</article>
|
||
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