# Command Line Interface

This page shows the MicroHapulator command line interface: how inputs and settings are specified for each subcommand.

**NOTE**: The MicroHapulator CLI is under [Semantic Versioning](https://semver.org/).
In brief, this means that every stable version of the MicroHapulator software is assigned a version number, and that any changes to the software's behavior or interface require the software version number to be updated in prescribed and predictable ways.

-----------

## End-to-end analysis workflow

### `mhpl8r pipe`

```{argparse}
:module: microhapulator.cli
:func: get_parser
:prog: mhpl8r
:path: pipe
:nodefault:
```


## Haplotype calling

### `mhpl8r type`

```{argparse}
:module: microhapulator.cli
:func: get_parser
:prog: mhpl8r
:path: type
:nodefault:
```

### `mhpl8r filter`

```{argparse}
:module: microhapulator.cli
:func: get_parser
:prog: mhpl8r
:path: filter
:nodefault:
```


## Analysis, QA/QC, and interpretation

### `mhpl8r locbalance`

```{argparse}
:module: microhapulator.cli
:func: get_parser
:prog: mhpl8r
:path: locbalance
:nodefault:
```

### `mhpl8r hetbalance`

```{argparse}
:module: microhapulator.cli
:func: get_parser
:prog: mhpl8r
:path: hetbalance
:nodefault:
```

### `mhpl8r offtarget`

```{argparse}
:module: microhapulator.cli
:func: get_parser
:prog: mhpl8r
:path: offtarget
:nodefault:
```

### `mhpl8r contrib`

```{argparse}
:module: microhapulator.cli
:func: get_parser
:prog: mhpl8r
:path: contrib
:nodefault:
```

### `mhpl8r prob`

```{argparse}
:module: microhapulator.cli
:func: get_parser
:prog: mhpl8r
:path: prob
:nodefault:
```

### `mhpl8r diff`

```{argparse}
:module: microhapulator.cli
:func: get_parser
:prog: mhpl8r
:path: diff
:nodefault:
```

### `mhpl8r dist`

```{argparse}
:module: microhapulator.cli
:func: get_parser
:prog: mhpl8r
:path: dist
:nodefault:
```

### `mhpl8r contain`

```{argparse}
:module: microhapulator.cli
:func: get_parser
:prog: mhpl8r
:path: contain
:nodefault:
```

### `mhpl8r convert`

```{argparse}
:module: microhapulator.cli
:func: get_parser
:prog: mhpl8r
:path: convert
:nodefault:
```

### `mhpl8r getrefr`

```{argparse}
:module: microhapulator.cli
:func: get_parser
:prog: mhpl8r
:path: getrefr
:nodefault:
```


## Simulation

### `mhpl8r sim`

```{argparse}
:module: microhapulator.cli
:func: get_parser
:prog: mhpl8r
:path: sim
:nodefault:
```

### `mhpl8r mix`

```{argparse}
:module: microhapulator.cli
:func: get_parser
:prog: mhpl8r
:path: mix
:nodefault:
```

### `mhpl8r unite`

```{argparse}
:module: microhapulator.cli
:func: get_parser
:prog: mhpl8r
:path: unite
:nodefault:
```

### `mhpl8r seq`

```{argparse}
:module: microhapulator.cli
:func: get_parser
:prog: mhpl8r
:path: seq
:nodefault:
```