alignoth 0.2.1

A tool for creating alignment plots from bam files
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# alignoth

A tool for creating alignment plots from bam files. The generated [vega-lite](https://vega.github.io/vega-lite/) plots are written to stdout per default.

## Usage

```alignoth -b path/to/my.bam -r path/to/my/reference.fa -g chr1:200-300 > plot.vl.json```

### Arguments

The following options are available when using bamboo:

| argument         | short | explanation                                                                                                 | default |
|------------------|-------|-------------------------------------------------------------------------------------------------------------|--------|
| bam_path         | -b    | The bam file to be visualized.                                                                              |        |
| reference        | -r    | The path to the reference fasta file                                                                        |        |
| region           | -g    | Chromosome and region for the visualization. Example: 2:132424-132924                                       |        |
| highlight        | -h    | Interval that will be highlighted in the visualization. Example: 132400-132500                              |        |
| max-read-depth   | -d    | Set the maximum rows of reads that will be shown in the alignment plots                                     | 500    |
| output           | -o    | If present, data and vega-lite specs of the generated plot will be split and written to the given directory |        |
| spec-output      |       | If present vega-lite specs will be written to the given file path                                           |        |
| read-data-output |       | If present read data will be written to the given file path                                                 |        |
| ref-data-output  |       | If present reference data will be written to the given file path                                            |        |

## Installation

There a multiple ways to install alignoth:

#### Bioconda

Rust-Bio-Tools is available via [Bioconda](https://bioconda.github.io).
With Bioconda set up, installation is as easy as

    conda install alignoth

#### Cargo

If the [Rust](https://www.rust-lang.org/tools/install) compiler and associated [Cargo](https://github.com/rust-lang/cargo/) are installed, alignoth may be installed via

    cargo install alignoth

#### Source

Download the source code and within the root directory of source run

    cargo install

## Authors

* [Felix Wiegand](https://github.com/fxwiegand)
* [Johannes Köster](https://github.com/johanneskoester) (https://koesterlab.github.io)