feat: add memory vectors, slice traits, and column extraction methods
Introduce `MemoryBitVec` and `MemoryIntVec` for efficient in-memory storage with hybrid compression and overflow handling. Implement `BitSlice`, `BitSliceMut`, `IntSlice`, and `IntSliceMut` traits across persistent and memory-backed types to enable generic slice operations and bitwise/arithmetic overloads. Add `col_persist` and `col_as_memory` methods to `BitMatrix` and `IntMatrix` for efficient column extraction. Align with the new single-pass rebuild architecture by supporting fast kmer filtering and matrix rebuilding. Includes comprehensive tests and profiling instrumentation for the packing phase.
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@@ -98,7 +98,9 @@ impl KmerIndex {
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fs::File::create(output.join(SENTINEL_INDEXED))?;
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let idx = KmerIndex::open(output)?;
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let t_pack = Stage::start("pack");
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idx.pack_matrices()?;
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rep.push(t_pack.stop());
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Ok(idx)
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}
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}
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