Eric Coissac
c694e1f2b0
Introduces a Make-based orchestration for simulating, indexing, merging, filtering, and verifying k-mer counts and presence. Exposes internal builder and iterator APIs publicly, enforces mandatory leading slashes for predicate patterns, registers the `obitaxonomy` crate, and updates tooling configurations alongside documentation.
112 lines
3.0 KiB
Rust
112 lines
3.0 KiB
Rust
use std::io;
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use std::path::Path;
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use tempfile::TempDir;
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use crate::bitvec::{PersistentBitVec, PersistentBitVecBuilder};
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use crate::views::{BitSliceIter, BitSliceView, IntSliceView};
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// ── TempBitVec — frozen read-only, auto-deleted on drop ──────────────────────
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pub struct TempBitVec {
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vec: PersistentBitVec,
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// Dropped after `vec` (field order), so the mmap is released before the
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// temp directory is deleted.
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_temp: TempDir,
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}
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impl TempBitVec {
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pub fn make_persistent(&self, path: &Path) -> io::Result<PersistentBitVec> {
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std::fs::copy(self.vec.path(), path)?;
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PersistentBitVec::open(path)
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}
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pub fn len(&self) -> usize {
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self.vec.len()
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}
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pub fn is_empty(&self) -> bool {
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self.vec.is_empty()
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}
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pub fn get(&self, slot: usize) -> bool {
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self.vec.get(slot)
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}
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pub fn count_ones(&self) -> u64 {
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self.vec.count_ones()
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}
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pub fn view(&self) -> BitSliceView<'_> {
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self.vec.view()
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}
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pub fn iter(&self) -> BitSliceIter<'_> {
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self.view().iter()
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}
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}
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// ── TempBitVecBuilder — mutable, becomes TempBitVec on freeze ────────────────
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pub struct TempBitVecBuilder {
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builder: PersistentBitVecBuilder,
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temp: TempDir,
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}
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impl TempBitVecBuilder {
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pub fn new(n: usize) -> io::Result<Self> {
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let temp = TempDir::new()?;
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let path = temp.path().join("data.pbiv");
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let builder = PersistentBitVecBuilder::new(n, &path)?;
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Ok(Self { builder, temp })
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}
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pub fn new_ones(n: usize) -> io::Result<Self> {
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let temp = TempDir::new()?;
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let path = temp.path().join("data.pbiv");
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let builder = PersistentBitVecBuilder::new_ones(n, &path)?;
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Ok(Self { builder, temp })
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}
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pub fn freeze(self) -> io::Result<TempBitVec> {
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let Self { builder, temp } = self;
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let vec = builder.finish()?;
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Ok(TempBitVec { vec, _temp: temp })
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}
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pub fn set(&mut self, slot: usize, value: bool) {
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self.builder.set(slot, value);
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}
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pub fn view(&self) -> BitSliceView<'_> {
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self.builder.view()
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}
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pub fn or(&mut self, other: BitSliceView<'_>) {
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self.builder.or(other);
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}
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pub fn and(&mut self, other: BitSliceView<'_>) {
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self.builder.and(other);
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}
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pub fn xor(&mut self, other: BitSliceView<'_>) {
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self.builder.xor(other);
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}
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pub fn not(&mut self) {
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self.builder.not();
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}
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pub fn copy_from(&mut self, src: BitSliceView<'_>) {
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self.builder.copy_from(src);
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}
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pub fn or_where(&mut self, col: IntSliceView<'_>, pred: impl Fn(u32) -> bool) {
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self.builder.or_where(col, pred);
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}
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pub fn and_where(&mut self, col: IntSliceView<'_>, pred: impl Fn(u32) -> bool) {
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self.builder.and_where(col, pred);
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}
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pub fn xor_where(&mut self, col: IntSliceView<'_>, pred: impl Fn(u32) -> bool) {
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self.builder.xor_where(col, pred);
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}
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}
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