Indel Mapper

Running Indel Mapper

Example:

$ pip3 install indel-mapper
$ indel-mapper -a ~/Documents/bowtie2_results.sam -r ~/Documents/references.csv -o ~/Documents/results.csv -m

There are three required arguments and one optional argument for generating the metadata:

• -a or --alignment Alignment SAM file
• -r or --reference Reference CSV file
• -o or --output Output file, in CSV
• -m or --metadata Include a metadata JSON in the output generation, for visualization

For Development

Set up

First, make sure the correct version of virtualenv is installed:

$ pip3 install virtualenv

Next, cd into your project and set up the virtualenv directory:

$ virtualenv --python=python3 .indel-mapper

Activate virtualenv. This adds the indel-mapper/bin directory to the start of your $PATH.

$ source .indel-mapper/bin/activate

Install the required libraries:

$ pip3 install -r requirements.txt

Run the tests:

$ python3 -m pytest

Releasing to PyPI

$ python3 setup.py sdist
$ twine upload dist/*

License

Indel Mapper is licensed under Version 3 of the GNU General Public License.