Metadata-Version: 2.1
Name: stranger
Version: 0.1
Summary: Annotate VCF files with str variants
Home-page: https://github.com/moonso/stranger
Author: Måns Magnusson
Author-email: mans.magnusson@scilifelab.com
License: MIT
Keywords: vcf,variants,str
Platform: UNKNOWN
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: Unix
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.6.0
Description-Content-Type: text/markdown
Requires-Dist: click
Requires-Dist: cyvcf2
Requires-Dist: coloredlogs
Requires-Dist: parse
Provides-Extra: tests
Requires-Dist: pytest ; extra == 'tests'


# Stranger

Annotates output files from [ExpansionHunter][hunter] with the pathologic implications of the repeat sizes.

## Installation

```
git clone github.com/moonso/stranger
cd stranger
pip install --editable .
```

## Usage

```
stranger --help
Usage: stranger [OPTIONS] VCF

  Annotate str variants with str status

Options:
  -f, --repeats-file PATH         Path to a file with repeat definitions. See
                                  README for explanation  [default: /Users/man
                                  smagnusson/Projects/stranger/stranger/resour
                                  ces/repeatexpansionsloci.tsv]
  --version
  --loglevel [DEBUG|INFO|WARNING|ERROR|CRITICAL]
                                  Set the level of log output.  [default:
                                  INFO]
  --help                          Show this message and exit.

```





[hunter]: https://github.com/Illumina/ExpansionHunter

