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