https://github.com/moold/hifiasm2txt
A small tool to convert hifiasm bin files to text format.
https://github.com/moold/hifiasm2txt
Last synced: 10 months ago
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A small tool to convert hifiasm bin files to text format.
- Host: GitHub
- URL: https://github.com/moold/hifiasm2txt
- Owner: moold
- License: gpl-3.0
- Created: 2024-07-09T14:20:28.000Z (almost 2 years ago)
- Default Branch: main
- Last Pushed: 2024-07-11T07:55:41.000Z (almost 2 years ago)
- Last Synced: 2025-04-06T10:41:31.007Z (about 1 year ago)
- Language: Rust
- Homepage:
- Size: 22.5 KB
- Stars: 5
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# hifiasm2txt
A small tool to convert hifiasm bin files (`ec.bin`, `ovlp.source.bin` and `ovlp.reverse.bin`) to text format.
- `ec.bin`: error corrected reads.
- `ovlp.source.bin`: overlaps between reads from the same haplotype (?).
- `ovlp.reverse.bin`: overlaps between reads from the different haplotype (?).
## Installation
#### Dependencies
`hifiasm2txt` is written in rust, try below commands (no root required) or see [here](https://www.rust-lang.org/tools/install) to install `Rust` first.
```
curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
```
#### Download and install
```
git clone git@github.com:moold/hifiasm2txt.git
cd hifiasm2txt && cargo build --release
```
*If you want to speed up downloading and compiling in China, please visit [here](https://mirrors.tuna.tsinghua.edu.cn/help/crates.io-index/) to set up a mirror (Tsinghua Open Source Mirror).*
## Usage
```
./target/release/hifiasm2txt path_to_hifiasm_workdir/hifiasm.asm --out_ec_bin --out_so_bin --out_re_bin
```
## Parameters
```
A small tool to convert hifiasm bin files to text (gzip) format.
Usage: hifiasm2txt [OPTIONS] [PREFIX]
Arguments:
output file path and prefix of `hifiasm`.
[PREFIX] prefix of output files. [default: hifiasm2txt]
Options:
-e, --out_ec_bin convert PATH/PREFIX.ec.bin file.
-r, --out_re_bin convert PATH/PREFIX.reverse.bin file.
-s, --out_so_bin convert PATH/PREFIX.source.bin file.
-h, --help Print help
-V, --version Print version
```