Eric Coissac
27f5e88a7b
Replace raw SuperkMer routing with a new RoutableSuperKimer type that embeds canonical sequences and precomputed minimizers, enabling direct partition routing via hash. Update the build pipeline to yield RoutableSuperKmers throughout (builder, scatterer), refactor FASTA/unitig export commands to use the new type and compressed outputs (.fasta.gz, .unitigs.fasta.zst), revise SuperKmer header to store n_kmers instead of seql (avoiding 256-byte wrap), and update documentation to reflect minimizer-based theory, two evidence-encoding strategies for unitig-MPHF indexing (global offset vs. ID+rank), and the new obipipeline library architecture with parallel workers, biased scheduling, and error handling.
1030 lines
20 KiB
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1030 lines
20 KiB
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On-disk storage
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Kmers and super-kmers
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DNA encoding
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Entropy filter
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Minimizer selection
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Partitioning architecture
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Implementation
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SuperKmer
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Kmer
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Chunk reader
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Construction pipeline
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obipipeline library
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</a>
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On-disk storage
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<span class="md-nav__icon md-icon"></span>
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On-disk storage
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</a>
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<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
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<label class="md-nav__title" for="__toc">
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<span class="md-nav__icon md-icon"></span>
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Table of contents
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<ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
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<li class="md-nav__item">
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<a href="#collection-parameters" class="md-nav__link">
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<span class="md-ellipsis">
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Collection parameters
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<li class="md-nav__item">
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<a href="#count-storage" class="md-nav__link">
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<span class="md-ellipsis">
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Count storage
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</a>
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<a href="#query-protocol" class="md-nav__link">
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<span class="md-ellipsis">
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Query protocol
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<span class="md-ellipsis">
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MPHF selection
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<span class="md-ellipsis">
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Unitig evidence encoding
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</span>
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</a>
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Architecture
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Architecture
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Sequences
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Table of contents
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Collection parameters
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Count storage
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Query protocol
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<article class="md-content__inner md-typeset">
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<h1 id="on-disk-collection-structure">On-disk collection structure</h1>
|
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<p>Collections are too large to hold in RAM (hundreds of genomes, billions of kmers). The collection lives on disk as a directory of memory-mapped files:</p>
|
||
<div class="highlight"><pre><span></span><code>collection/
|
||
metadata.toml — collection parameters (see below)
|
||
part_XXXX/
|
||
superkmers.bin.gz — dereplicated super-kmers for this partition (construction artifact)
|
||
mphf.bin — minimal perfect hash function for this partition
|
||
counts.bin — packed n-bit count array (or 1-bit presence array)
|
||
refs.bin — back-references u32 nucleotide offset into unitigs.bin per kmer
|
||
unitigs.bin — local de Bruijn unitigs (permanent evidence structure)
|
||
overflow.bin — counts exceeding the packed range (optional)
|
||
</code></pre></div>
|
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<p><code>superkmers.bin.gz</code> is produced during phase 1 and consumed through phases 2–4. It can be deleted after phase 5 — it is not needed for querying. The permanent query structure is <code>mphf.bin + counts.bin + refs.bin + unitigs.bin</code>.</p>
|
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<h2 id="collection-parameters">Collection parameters</h2>
|
||
<p>Stored in <code>metadata.toml</code>:</p>
|
||
<table>
|
||
<thead>
|
||
<tr>
|
||
<th>Parameter</th>
|
||
<th>Role</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr>
|
||
<td>k</td>
|
||
<td>kmer length</td>
|
||
</tr>
|
||
<tr>
|
||
<td>m</td>
|
||
<td>minimizer length (odd, < k)</td>
|
||
</tr>
|
||
<tr>
|
||
<td>p</td>
|
||
<td>partition bits (0 ≤ p ≤ min(14, 2m−16))</td>
|
||
</tr>
|
||
<tr>
|
||
<td>mode</td>
|
||
<td><code>presence</code> (1 bit/kmer) or <code>count</code> (n bits/kmer)</td>
|
||
</tr>
|
||
<tr>
|
||
<td>n</td>
|
||
<td>bits per kmer in count mode (chosen at construction)</td>
|
||
</tr>
|
||
<tr>
|
||
<td>min_count</td>
|
||
<td>singleton filtering threshold (0 = keep all)</td>
|
||
</tr>
|
||
<tr>
|
||
<td>hash_fn</td>
|
||
<td>hash function identifier</td>
|
||
</tr>
|
||
<tr>
|
||
<td>hash_seed</td>
|
||
<td>seed for the hash function</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
<h2 id="count-storage">Count storage</h2>
|
||
<p><strong>refs.bin capacity:</strong> <code>unitigs.bin</code> is a flat 2-bit-packed nucleotide stream with no separators. Each entry in <code>refs.bin</code> is a u32 nucleotide offset pointing to the first base of the kmer. A u32 covers 4 billion nucleotide positions = 1 GB of sequence per partition. In the worst case (all unitigs of length 1 kmer, offsets spaced k apart), this supports 4 billion / k ≈ 130 million kmers per partition at k=31. In the typical case (long unitigs, consecutive kmers at offset +1), the limit approaches 4 billion kmers — well beyond any realistic partition size.</p>
|
||
<p><em>Presence mode</em> (coverage ≤ 1x, or when only presence/absence matters):</p>
|
||
<ul>
|
||
<li><code>counts.bin</code> is a packed 1-bit array — all bits set to 1 for indexed kmers</li>
|
||
<li>Singletons are the signal, not filtered</li>
|
||
</ul>
|
||
<p><em>Count mode</em> (coverage > 1x):</p>
|
||
<ul>
|
||
<li><code>counts.bin</code> is a packed n-bit array; n chosen at construction from the observed distribution</li>
|
||
<li>Value 0: absent sentinel; values 1..2ⁿ−2: direct count; value 2ⁿ−1: overflow</li>
|
||
<li>Overflow counts stored in a separate <code>overflow.bin</code> as sorted <code>(index: u32, count: u32)</code> pairs</li>
|
||
<li>Empirically (k=31, 15x coverage): n=5 covers 97% of real kmers, n=6 covers 99%</li>
|
||
<li>min_count threshold filters low-frequency kmers (errors) before indexing; for ≤1x, min_count=0</li>
|
||
</ul>
|
||
<h2 id="query-protocol">Query protocol</h2>
|
||
<div class="highlight"><pre><span></span><code>query kmer q
|
||
→ canonical_minimizer(q) → hash → PART → part_XXXX/
|
||
→ MPHF(q) → index i
|
||
→ refs[i] = (unitig_id, kmer_offset)
|
||
→ read unitig from unitigs.bin → extract kmer at kmer_offset → compare with q
|
||
→ match : return counts[i]
|
||
→ no match: kmer absent
|
||
</code></pre></div>
|
||
|
||
|
||
|
||
|
||
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