# rspoa
POA in Rust
## Usage
After cloning the repository from GitHub, move to its main directory and compile the package with
```
cargo build --release
```
To use rspoa you need a .gfa file and a .fasta file containing the reads you want to align to the graph. In order to run rspoa:
```
cargo run --release <reads.fa> <graph.gfa>
```
You can set different parameters and choose between different alignment types:
```
OPTIONS:
-h, --help Print help information
-V, --version Print version information
I/O:
<SEQUENCE_PATH> Sequences to align file path
<GRAPH_PATH> Graph file path
-o, --out_file <OUT_FILE> Specifies the output file, if not indicated prints in standard
output [default: "standard output"]
Alignment:
-m, --aln-mode <ALIGNMENT_MODE> 0: global, 1: local, 2: affine gap, 3: local gap,
4: pathwise alignment[DEMO],
-M, --match <MATCH_SCORE> Match score [default: 2]
-X, --mismatch <MISMATCH_SCORE> Mismatch penalty [default: 4]
-O, --gap-open <GAP_OPEN> Gap opening penalty [default: 4]
-E, --gap-ext <GAP_EXTENSION> Gap extension penalty [default: 2]
-s, --amb-strand <AMB_STRAND> Ambigous strand mode, try reverse complement if
alignment score is too low [default: false] [possible values:
true, false]
-t, --matrix <MATRIX> Scoring matrix file, if '-t' is used '-M' and '-X' are not
used. You should set appropriate gap penalties if aln-mode is
2 or 3[default: none]
Adaptive banded:
-b, --extra-b <EXTRA_B> First adaptive banding parameter, set < 0 to disable adaptive banded
[default: 1]
-f, --extra-f <EXTRA_F> Second adaptive banding parameter, number of basis added to both side of
the band = b+f*L, l = length of the sequence [default: 0.01]
```
The output is in .gaf format, in reference to the graph in input.
```
>read1 50 0 50 + >1>3>5>6>8>9>11>12>13>15>16>18>19 50 0 11 49 * * 8M,1M,1M,3M,1M,4M,5M,2M,8M,1M,4M,1M,11M
```
### Library
rsPOA can also be used as a library for your project.
In order to do so add to your Cargo.toml file:
```
[dependencies]
rspoa= { git = "https://github.com/AlgoLab/rspoa" }
```
In this case you can use the functions inside the api.rs file, they need only the read as a string and the graph as an HashGraph, other parameters can be set or left by default.
You can use them by adding ```use rspoa::api::*``` in your file.