Split sample SNP evidence files into bins for EFM (#58)

.github/workflows/cibuild.yml

@@ -19,7 +19,7 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install
       run: |
-        python -m pip install --upgrade pip pytest pytest-cov black==22.6
+        pip install --upgrade pip pytest pytest-cov black==22.6
         pip install .
     - name: Style check
       run: make style

.gitignore

@@ -1,3 +1,4 @@
 __pycache__/
 lusSTR.egg-info/
 .coverage
+sandbox/

Makefile

@@ -6,7 +6,7 @@ help: Makefile
 
 ## test:      run the automated test suite and print coverage information
 test:
-	pytest -m "not snps" --cov=lusSTR --doctest-modules lusSTR/tests/test_*.py
+	pytest --cov=lusSTR --doctest-modules lusSTR/tests/test_*.py
 
 ## style:     check code style
 style:

lusSTR/cli/config.py

@@ -134,7 +134,8 @@ def subparser(subparsers):
     )
     p.add_argument(
         "--separate", action="store_true", 
-        help="Use to separate EFM profiles in the 'filter' step."
+        help="Use to separate EFM profiles in the 'filter' step. If specifying for SNPs, "
+        "each sample will also be separated into 10 different bins for mixture deconvolution."
     )
     p.add_argument(
         "--nofiltering", action="store_true",