Crate psltools 

psltools

A high-performance library and CLI for the PSL alignment format (BLAT/lastz output), modeled on chaintools.

Design

• Zero-copy parsing. Names and PSLx sequence columns are ByteSlice views into a shared (memory-mapped or owned) buffer; the three block coordinate lists live in one structure-of-arrays arena. The whole-file Reader allocates nothing per record.
• One record per line. Unlike chain, a PSL record is a single line, so parsing chunks in parallel, indexing, and streaming are all simple.
• Kent-exact scoring. psl_score / milli_bad / percent_id reproduce kent/src/lib/psl.c bit-for-bit (including repMatch >> 1, sizeMul derivation, and i32 integer semantics).
• Correctness on the hard corners. Negative-strand qStarts/tStarts, translated (two-char) strands, and PSLx sequence columns are handled in the model from the start.

Quick start

use psltools::Reader;

let reader = Reader::<psltools::Psl>::from_path("example.psl")?;
for psl in reader.records() {
    println!(
        "{} -> {}  score={}",
        psl.query_name_str(),
        psl.reference_name_str(),
        psl.score()
    );
}

Feature flags

• mmap (default): memory-map inputs for zero-copy parsing.
• cli (default): build the psltools binary (implies parallel).
• gzip: transparently read/write .gz PSL.
• parallel: multi-threaded parsing and parallel record iteration.
• index: record-offset and interval indexes.
• serde: derive Serialize/Deserialize on the owned types.
• bigcoords: widen Coord to u64 for exotic assemblies.

Re-exports

pub use model::Coord;

pub use model::block::Block;

pub use model::block::BlockSlice;

pub use model::block::Blocks;

pub use model::error::PslError;

pub use model::psl::Psl;

pub use model::psl::PslFlavor;

pub use model::psl::PslRecord;

pub use model::psl::PslxSeq;

pub use model::psl::Strand;

pub use model::psl::Strands;

pub use io::reader::Reader;

pub use io::reader::ReaderOptions;

pub use io::storage::ByteSlice;

pub use io::storage::SharedBytes;

pub use io::stream::OwnedBlocks;

pub use io::stream::OwnedPsl;

pub use io::stream::OwnedPslHeader;

pub use io::stream::StreamItem;

pub use io::stream::StreamingReader;

pub use io::writer::PslWriter;

pub use io::writer::write_psl;

pub use io::writer::write_psl_header;

pub use ops::check::CheckReport;

pub use ops::check::check;

pub use ops::convert::to_bed;

pub use ops::convert::to_bed12;

pub use ops::convert::to_genepred;

pub use ops::score::ScoreOpts;

pub use ops::score::milli_bad;

pub use ops::score::percent_id;

pub use ops::score::psl_score;

pub use ops::swap::swap;

pub use ops::swap::swap_with;

pub use genepred;

Modules

io

PSL input/output.

model

Core PSL data model.

ops

Record-level operations shared by library users and the CLI.

parser

PSL parsing primitives.