seqwish 0.1.3

A variation graph inducer - build pangenome graphs from pairwise alignments
Documentation 
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[package]
name = "seqwish"
version = "0.1.3"
edition = "2021"
authors = ["Erik Garrison <erik.garrison@gmail.com>"]
description = "A variation graph inducer - build pangenome graphs from pairwise alignments"
repository = "https://github.com/pangenome/seqwish"
license = "MIT"
keywords = ["bioinformatics", "genomics", "pangenome", "variation-graph", "gfa"]
categories = ["science", "command-line-utilities"]
readme = "README.md"
rust-version = "1.70"
exclude = [
    "test/*",
    "data/*",
    "cpp/*",
    "deps/**/*",        # Exclude all C++ dependencies
    "scripts/*",        # Exclude helper scripts
    "examples/*",       # Exclude examples
    "*.pdf",
    "*.md",
    "!README.md",
    ".github/*",
    ".claude/*",
    "Dockerfile",
    "*.log",            # Exclude log files
    "benchmark_*.log",
    "target/**/*",      # Exclude build artifacts
    "SEQINDEX_ANALYSIS_FINAL_REPORT.txt",
    ".gitmodules",      # Don't need git submodule info
    ".gitignore",
    "default.nix",      # Nix files not needed
    "seqwish.nix",
]

[lib]
crate-type = ["rlib", "staticlib", "cdylib"]

[[bin]]
name = "seqwish"
path = "src/main.rs"

[dependencies]
libc = "0.2"
once_cell = "1.21"
memmap2 = "0.9"
flate2 = "1.0"  # For gzip support
fm-index = "0.3"  # FM-index / CSA for sequence name lookup
vers-vecs = { version = "1.1", features = ["simd"] }  # Succinct bitvectors with rank/select (SIMD-accelerated)
iitree-rs = "0.1.1"  # Interval tree with disk-backed storage

# Transclosure dependencies
rayon = "1.11"                  # Parallel iteration & sorting
crossbeam-queue = "0.3"         # Lock-free queues
bitvec = { version = "1.0", features = ["atomic"] }  # Atomic bitvector
parking_lot = "0.12"            # Fast mutexes
sucds = "0.8"                   # Succinct data structures (rank/select)
uf_rush = "0.1"                 # Lock-free union-find
rdst = "0.20"                    # Fast parallel radix sort
portable-atomic = "1.9"         # 128-bit atomics for dset64

# CLI dependencies
clap = { version = "4.5", features = ["derive"] }  # Command-line argument parsing

[build-dependencies]
cbindgen = "0.27"