refactor: implement RoutableSuperKmer and update k-mer indexing pipeline
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.
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@@ -12,7 +12,7 @@
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<link rel="prev" href="../chunkreader/">
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<link rel="next" href="../storage/">
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<link rel="next" href="../obipipeline/">
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@@ -230,7 +230,7 @@
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<li class="md-nav__item">
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<a href="../../theory/kmers/" class="md-nav__link">
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<a href="../../kmers/" class="md-nav__link">
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@@ -313,6 +313,34 @@
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<li class="md-nav__item">
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<a href="../../theory/minimizer/" class="md-nav__link">
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<span class="md-ellipsis">
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Minimizer selection
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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="../../theory/indexing/" class="md-nav__link">
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@@ -633,6 +661,34 @@
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<li class="md-nav__item">
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<a href="../obipipeline/" class="md-nav__link">
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<span class="md-ellipsis">
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obipipeline library
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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="../storage/" class="md-nav__link">
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@@ -683,6 +739,34 @@
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<li class="md-nav__item">
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<a href="../unitig_evidence/" class="md-nav__link">
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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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</li>
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</ul>
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</nav>
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