https://github.com/andreaguarracino/cigzip
https://github.com/andreaguarracino/cigzip
Last synced: 3 months ago
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- Host: GitHub
- URL: https://github.com/andreaguarracino/cigzip
- Owner: AndreaGuarracino
- License: mit
- Created: 2025-02-18T13:05:13.000Z (3 months ago)
- Default Branch: main
- Last Pushed: 2025-02-26T20:46:55.000Z (3 months ago)
- Last Synced: 2025-02-26T21:22:51.367Z (3 months ago)
- Language: Rust
- Size: 121 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# cigzip
A tool for compression and decompression of alignment CIGAR strings using tracepoints.
## Overview
`cigzip` leverages an efficient approach to sequence alignment storage using tracepoints. Instead of storing complete CIGAR strings, alignments are compressed into tracepoints that adapt to the local alignment complexity, reducing storage size while allowing for full reconstruction.
## Features
- **Compression**: Convert CIGAR strings to tracepoints for compact storage
- **Decompression**: Reconstruct full CIGAR strings from tracepoints
- **Multiple Banding Strategies**: Choose between no banding, single-band, or double-band tracepoints
- **Parallel Processing**: Multi-threaded operation with chunk-based processing
- **Configurable Parameters**: Adjust max-diff, gap penalties, and other settings
- **Support for Compressed Files**: Automatically handles gzipped and bgzipped PAF files
## Usage
```shell
# Compress alignments in a PAF file (convert CIGAR to tracepoints)
cigzip compress --paf alignments.paf [--band none|single|double] [--max-diff 128] [--threads 4] > alignments.tp.paf
# Decompress alignments (convert tracepoints back to CIGAR)
cigzip decompress --paf alignments.tp.paf --fasta sequences.fa [--penalties "3,4,2,24,1"] [--threads 4] > alignments.cigar.paf
```
## Building
You need to build `WFA2-lib` first, which is a submodule of this repository. To do so, run:
```shell
git clone --recursive https://github.com/AndreaGuarracino/cigzip
cd cigzip/WFA2-lib
make clean all
cd ..
```
Then, you can build the project using Cargo:
```shell
# Point to your pre-built WFA2-lib directory
export WFA2LIB_PATH="./WFA2-lib"
# Build your project
cargo build --release
```
### For GUIX's slaves
```bash
git clone --recursive https://github.com/AndreaGuarracino/cigzip
cd cigzip/WFA2-lib
guix shell -C -D -f guix.scm
export CC=gcc; make clean all
exit
cd ..
env -i bash -c 'WFA2LIB_PATH="./WFA2-lib" PATH=/usr/local/bin:/usr/bin:/bin ~/.cargo/bin/cargo build --release'
```
## License
This project is licensed under the MIT License. See the [LICENSE](LICENSE) file for details.
## References
Inspired by Gene Myers' tracepoint concept described in [Recording Alignments with Trace Points](https://dazzlerblog.wordpress.com/2015/11/05/trace-points/).