Quick Start

The fastest path: build an index on the CPU and run a couple of queries.

Build and query (CPU)

use haystackfm::{DnaSequence, FmIndex, FmIndexConfig};

let seq = DnaSequence::from_str("ACGTACGT")?;
let config = FmIndexConfig::default();
let index = FmIndex::build_cpu(&[seq], &config)?;

// A DnaSequence holds IUPAC-encoded bytes; encode the query the same way.
let query = DnaSequence::from_str("ACGT")?;

assert_eq!(index.count(query.as_slice()), 2);
let positions = index.locate(query.as_slice()); // Vec<(SeqId, u32)> — (seq id, offset)

count returns how many times the pattern occurs; locate returns the (SeqId, offset) of each occurrence. A SeqId is the reference’s 0-based position in build order, not its FASTA name — resolve one with index.seq_header(id), and go the other way with index.seq_id("chr1"). See Sequence ids vs. headers for why, and Count & Locate for the full surface.

Build on the GPU

GPU construction is async and returns the same FmIndex type:

use haystackfm::{DnaSequence, FmIndex, FmIndexConfig};
use haystackfm::gpu::locate::locate_batch_gpu;

let seqs = vec![DnaSequence::from_str("ACGTACGT")?];
let config = FmIndexConfig::default();

let index = FmIndex::build(&seqs, &config).await?;   // async GPU build

// Batched, IUPAC-aware GPU locate
let ctx = haystackfm::gpu::GpuContext::new().await?;
let query = DnaSequence::from_str("ACGT")?;
let queries: Vec<&[u8]> = vec![query.as_slice()];
let hits = locate_batch_gpu(&ctx, &index, &queries).await?;
// hits[i] = Vec<(seq_id, offset_within_seq)>

Requires the gpu feature. See GPU Acceleration.

Prefer the browser?

The live demo does all of this — build (CPU or GPU), search, serialize — without leaving the page. It’s the quickest way to see haystackfm run.

Configuration

FmIndexConfig::default() is a sensible starting point. The knobs that matter most:

let config = FmIndexConfig {
    sa_sample_rate: 4,
    ..Default::default()
};