https://github.com/andreaguarracino/lib_tracepoints
Compressed alignment representation
https://github.com/andreaguarracino/lib_tracepoints
Last synced: 4 months ago
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Compressed alignment representation
- Host: GitHub
- URL: https://github.com/andreaguarracino/lib_tracepoints
- Owner: AndreaGuarracino
- License: mit
- Created: 2025-02-26T09:52:49.000Z (4 months ago)
- Default Branch: master
- Last Pushed: 2025-02-26T11:03:33.000Z (4 months ago)
- Last Synced: 2025-02-26T11:27:07.741Z (4 months ago)
- Language: Rust
- Size: 9.77 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# lib_tracepoints
A Rust library for compressed alignment representation using tracepoints.
## Overview
`lib_tracepoints` provides utilities for converting between CIGAR strings and tracepoints for efficient alignment representation in bioinformatics applications. The library enables:
- Converting CIGAR strings to tracepoints
- Reconstructing CIGAR strings from tracepoints
- Managing tracepoints with configurable difference thresholds
- Tuning alignment compression/decompression with diagonal boundary tracking (single- or double-band)
## Installation
Add this to your `Cargo.toml`:
```toml
[dependencies]
lib_tracepoints = { git = "https://github.com/AndreaGuarracino/lib_tracepoints" }
```
## Dependencies
This library depends on `lib_wfa2`, which requires the `WFA2-lib` to be built first:
```shell
git clone https://github.com/smarco/WFA2-lib
cd WFA2-lib
make clean all
```
Then build your project with:
```shell
# Point to your pre-built WFA2-lib directory
export WFA2LIB_PATH="/path/to/WFA2-lib"
# Build your project
cargo build --release
```
## Usage
### Basic tracepoints
```rust
use lib_tracepoints::{cigar_to_tracepoints, tracepoints_to_cigar};
fn main() {
// Convert CIGAR to tracepoints with max difference of 5
let cigar = "10=2D5=2I3=";
let tracepoints = cigar_to_tracepoints(&cigar, 5);
// Reconstruct CIGAR from tracepoints
let a_seq = "ACGTACGTACACGTACGTAC";
let b_seq = "ACGTACGTACACGTACGTAC";
let reconstructed_cigar = tracepoints_to_cigar(
&tracepoints,
a_seq.as_bytes(),
b_seq.as_bytes(),
0, // a_start
0, // b_start
2, // mismatch penalty
4, // gap_open1
2, // gap_ext1
6, // gap_open2
1, // gap_ext2
);
}
```
### Double-band tracepoints
This approach stores both the minimum and maximum diagonal boundaries for each tracepoint. It provides more detailed boundary information for faster CIGAR string reconstruction but results in a slightly larger alignment representation.
```rust
use lib_tracepoints::{cigar_to_double_band_tracepoints, double_band_tracepoints_to_cigar};
fn main() {
let cigar = "10=2D5=2I3=";
// Store both min and max diagonal boundaries
let tracepoints: Vec<(usize, usize, (isize, isize))> =
cigar_to_double_band_tracepoints(cigar, 5);
let a_seq = "ACGTACGTACACGTACGTAC";
let b_seq = "ACGTACGTACACGTACGTAC";
let reconstructed_cigar = double_band_tracepoints_to_cigar(
&tracepoints,
a_seq.as_bytes(),
b_seq.as_bytes(),
0, 0, 2, 4, 2, 6, 1
);
}
```
### Single-band tracepoints
This approach stores only the maximum absolute diagonal boundary for each tracepoint. It's more memory-efficient but may require more computation during alignment reconstruction.
```rust
use lib_tracepoints::{cigar_to_single_band_tracepoints, single_band_tracepoints_to_cigar};
fn main() {
let cigar = "10=2D5=2I3=";
// Store only the maximum absolute diagonal value (more compact)
let single_band_tracepoints: Vec<(usize, usize, usize)> =
cigar_to_single_band_tracepoints(cigar, 5);
let a_seq = "ACGTACGTACACGTACGTAC";
let b_seq = "ACGTACGTACACGTACGTAC";
let reconstructed_cigar = single_band_tracepoints_to_cigar(
&single_band_tracepoints,
a_seq.as_bytes(),
b_seq.as_bytes(),
0, 0, 2, 4, 2, 6, 1
);
}
```