Merge branch '1-integrate-with-optispeed' into 'master'

Resolve "integrate with optispeed"

Closes #1

See merge request !2

README.md

+# OptiMap - Optical-map moleculue alignment tool
+
+## Requirements:
+
+Depends on [OptiScan](https://gitlab.com/akdel/OptiScan)
+
+## Installation
+
+```shell script
+git clone https://gitlab.com/akdel/OptiMap.git
+cd OptiMap
+pip install .
+```
+
+## Test with toy data
+```shell script
+OptiSpeed ./data/molecules.npy --first_score=0.8 --second_score=0.75 --output_filename=test_output.tsv --combine_sparse=True
+OptiSpeed ./data/molecules.bnx --first_score=0.8 --second_score=0.75 --output_filename=test_output.tsv --combine_sparse=True
+```
\ No newline at end of file

bin/OptiMap-deep.py → bin/OptiMap-deep

+#!/usr/bin/env python3
+
 import fire
 from OptiMap.OptiSpeed import compression as comp
 from OptiMap.OptiSpeed import square_wave as sw

bin/OptiMap-naive.py → bin/OptiMap-naive

+#!/usr/bin/env python3
+
 import fire
 from OptiMap.OptiSpeed import compression as comp
 from OptiMap.OptiSpeed import square_wave as sw

bin/OptiMap-sparse.py → bin/OptiMap-sparse

+#!/usr/bin/env python3
+
 import fire
 from OptiMap import correlation_struct as cs
 from OptiMap import molecule_struct as ms

bin/OptiSpeed.py → bin/OptiSpeed

+#!/usr/bin/env python3
+
 import fire
 from OptiMap.OptiSpeed import compression as comp
 from OptiMap.OptiSpeed import square_wave as sw

setup.py

@@ -6,6 +6,10 @@ setup(name='OptiMap',
       author='Mehmet Akdel',
       author_email='mehmet.akdel@wur.nl',
       url='https://gitlab.com/akdel/',
+      scripts=["bin/OptiMap-deep",
+               "bin/OptiMap-naive",
+               "bin/OptiMap-sparse",
+               "bin/OptiSpeed"],
       packages=['OptiMap', "OptiMap/OptiSpeed"],
       install_requires=["sqlalchemy", "numpy", "numba", "scipy", "intervaltree",
                         "matplotlib", "cython", "Simple-LSH", "fire", "ray"])