Eric Coissac
947 lines
19 KiB
HTML
947 lines
19 KiB
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obikmer
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MPHF selection
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obikmer
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Theory
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Kmers and super-kmers
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</a>
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DNA encoding
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</span>
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</a>
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Entropy filter
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</span>
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</a>
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Partitioning architecture
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</span>
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Implementation
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Implementation
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SuperKmer
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</span>
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</a>
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</li>
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Kmer
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</span>
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</a>
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<span class="md-ellipsis">
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Chunk reader
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</span>
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</a>
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<span class="md-ellipsis">
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Construction pipeline
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</span>
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</a>
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<li class="md-nav__item">
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<a href="../storage/" class="md-nav__link">
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<span class="md-ellipsis">
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On-disk storage
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</span>
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</a>
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<span class="md-ellipsis">
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MPHF selection
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</span>
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<span class="md-nav__icon md-icon"></span>
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<span class="md-ellipsis">
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MPHF selection
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</span>
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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="#candidates" class="md-nav__link">
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<span class="md-ellipsis">
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Candidates
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</span>
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</a>
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</li>
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<li class="md-nav__item">
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<a href="#space-at-scale" class="md-nav__link">
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<span class="md-ellipsis">
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Space at scale
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</span>
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</a>
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</li>
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<li class="md-nav__item">
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<a href="#on-disk-and-mmap-considerations" class="md-nav__link">
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<span class="md-ellipsis">
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On-disk and mmap considerations
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</span>
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</a>
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<li class="md-nav__item">
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<a href="#open-questions" class="md-nav__link">
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<span class="md-ellipsis">
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Open questions
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</a>
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<span class="md-ellipsis">
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Architecture
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<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
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<label class="md-nav__title" for="__nav_4">
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<span class="md-nav__icon md-icon"></span>
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Architecture
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<ul class="md-nav__list" data-md-scrollfix>
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<span class="md-ellipsis">
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Sequences
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</span>
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</a>
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Table of contents
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Candidates
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Space at scale
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On-disk and mmap considerations
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Open questions
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<h1 id="mphf-selection-analysis-in-progress">MPHF selection — analysis in progress</h1>
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<p>The choice of Minimal Perfect Hash Function for phase 6 is not yet settled. Three candidates were evaluated.</p>
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<h2 id="candidates">Candidates</h2>
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<p><strong>boomphf</strong> (BBHash algorithm, maintained by 10X Genomics):</p>
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<ul>
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<li>~3.7 bits/key; mature crate, used in production bioinformatics (Pufferfish, Piscem)</li>
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<li>Parallel construction; well-tested with DNA kmer data at scale</li>
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<li>Drawback: largest space footprint of the three</li>
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</ul>
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<p><strong>ptr_hash</strong> (PtrHash algorithm, Groot Koerkamp, SEA 2025):</p>
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<ul>
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<li>~2.4 bits/key; fastest queries (≥2.1× over alternatives, 8–12 ns/key for u64 in tight loops) and fastest construction (≥3.1×)</li>
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<li>Theoretical foundation solid; paper and Rust crate from the same author</li>
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<li>Drawback: published February 2025 — very young, no production track record</li>
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</ul>
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<p><strong>FMPHGO</strong> (<code>ph</code> crate, Beling, ACM JEA 2023):</p>
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<ul>
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<li>~2.1 bits/key — most compact of the three; good query speed; parallelisable construction</li>
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<li>More established than ptr_hash; actively maintained</li>
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<li>Currently preferred candidate</li>
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</ul>
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<h2 id="space-at-scale">Space at scale</h2>
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<p>For 1 024 partitions × 100 M kmers/partition:</p>
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<table>
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<thead>
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<tr>
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<th>MPHF</th>
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<th>bits/key</th>
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<th>Total MPHF size</th>
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</tr>
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</thead>
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<tbody>
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<tr>
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<td>boomphf</td>
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<td>3.7</td>
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<td>~47 GB</td>
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</tr>
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<tr>
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<td>ptr_hash</td>
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<td>2.4</td>
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<td>~31 GB</td>
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</tr>
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<tr>
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<td>FMPHGO</td>
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<td>2.1</td>
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<td>~27 GB</td>
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</tr>
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</tbody>
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</table>
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<p>In practice, partition sizes depend on the dataset. For a human genome at 30× coverage with p=10 (1 024 partitions), realistic partition sizes are 3–30 M kmers → 1–8 MB per MPHF, well within RAM.</p>
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<h2 id="on-disk-and-mmap-considerations">On-disk and mmap considerations</h2>
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<p>All three are in-memory structures. Their internal representation is flat bit arrays (no heap pointers), making them serialisable as contiguous byte blobs and mmappable per partition. True zero-copy access would require rkyv integration; the <code>ph</code> crate currently uses serde, so loading involves a copy. Given per-partition MPHF sizes of 1–8 MB, the OS page cache handles this transparently — strict zero-copy is a refinement, not a blocker.</p>
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<p>No established Rust crate provides a natively on-disk MPHF. <strong>SSHash</strong> (Sparse and Skew Hash) is a complete kmer dictionary designed for disk access and is order-preserving (overlapping kmers receive consecutive indices → cache-friendly count access), but it is C++-only and covers more than just the MPHF layer.</p>
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<h2 id="open-questions">Open questions</h2>
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<ul>
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<li>Confirm actual partition sizes on representative metagenomic datasets before fixing the choice.</li>
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<li>Evaluate whether ptr_hash's query speed advantage (2.1–3.3×) justifies adopting a crate that is less than a year old.</li>
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<li>Assess rkyv integration cost for FMPHGO if true zero-copy mmap becomes necessary.</li>
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<li>Keep SSHash in mind if the indexing architecture is reconsidered at a higher level.</li>
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</ul>
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