https://github.com/moold/map2ava
Convert read-to-ref mapping to read-vs-read overlapping
https://github.com/moold/map2ava
Last synced: 8 months ago
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Convert read-to-ref mapping to read-vs-read overlapping
- Host: GitHub
- URL: https://github.com/moold/map2ava
- Owner: moold
- License: gpl-3.0
- Created: 2022-02-22T07:10:12.000Z (over 4 years ago)
- Default Branch: main
- Last Pushed: 2022-08-10T08:14:37.000Z (almost 4 years ago)
- Last Synced: 2025-02-10T14:42:43.784Z (over 1 year ago)
- Language: Rust
- Size: 29.3 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# map2ava
Convert read-to-ref mapping to read-vs-read overlapping. If the mapping regions of two reads overlap, then the overlapping region/positions of these two reads can be calculated by their mapping CIGARs.
## Installation
#### Dependencies
`map2ava` 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 https://github.com/moold/map2ava.git
cd map2ava && cargo build --release
```
## Usage
`./target/release/map2ava --thread 20 input.map.bam > input.overlap.paf`
## Parameters
Use `./target/release/map2ava -h` to see options.