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added 30 commits
January 12, 2025 23:24
Piscem-cpp now relies on the main branch of @jermp's upstream SSHash.
This release finally moves to a piscem-cpp dependency that uses the offical sshash main branch! This means that sshash is no longer vendored or based on a fork. Changes to the sshash index mean that any piscem indices built with version < 0.13.0 must be rebuilt. This release also adds a new output file, <BASE>_ver.json which records the information of the piscem version with which the index was built, as well as the submodule commit hashes for the cuttlefish and piscem-cpp dependencies. Finally, this release updates piscem itself to the Rust 2024 edition.
When -o specifies a prefix whose parent directories don't yet exist, recursively create them before proceeding. Logs the creation via info!(). Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
CMake ExternalProject clones KMC into the source tree (cuttlefish/external/KMC) but tracks completion via stamp files in the cargo build directory. When cargo assigns a new build hash (e.g. after `cargo update`), the stamp files are lost but the cloned directory persists, causing `git clone` to fail. Detect this stale state (KMC dir exists but no CMakeCache.txt in the new build dir) and remove the old clone before cmake runs. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…ted scATAC flags Structural constraints are now supported by piscem-rs for bulk and scRNA mapping. Pass the flag through to MapBulkArgs and MapScrnaArgs instead of warning and ignoring. scATAC-only flags (--struct-constraints, --sam-format, --bed-format, --use-chr, --check-kmer-orphan) remain deprecated and hidden. Also adds [workspace] to Cargo.toml to prevent parent workspace auto-discovery, and updates piscem-rs git dep to ecd07f15. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Use the published crate instead of a git dependency. Move the cuttlefish-ver env var from .cargo/config.toml into build.rs, then gitignore .cargo/config.toml so it can hold a local-only [patch.crates-io] override for development without being checked in. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Instead of hardcoding the cuttlefish version in build.rs, run `git -C cuttlefish rev-parse HEAD` to read it from the submodule. Re-runs automatically when the submodule ref changes via rerun-if-changed on .git/modules/cuttlefish/HEAD. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Replace piscem-cpp FFI with piscem-rs library
ensure_simd (via packed-seq) checks CARGO_CFG_TARGET_FEATURE for "avx2" at compile time. This variable is only populated from explicit -C target-feature=+avx2 flags; -C target-cpu=x86-64-v3 alone does not cause Cargo to advertise AVX2 to build scripts. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Updated README with improved descriptions and build instructions.
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