Add usage doc

docs/source/API.rst

@@ -0,0 +1,5 @@
+API
+===
+
+.. automodule:: pydamage.main
+    :members:

docs/source/CLI.md

@@ -0,0 +1,32 @@
+# CLI
+
+Command Line Interface
+
+```bash
+$ pydamage --help
+Usage: pydamage [OPTIONS] BAM
+
+  PyDamage: Damage parameter estimation for ancient DNA
+  Author: Maxime Borry
+  Contact: <borry[at]shh.mpg.de>
+  Homepage & Documentation: github.com/maxibor/pydamage
+
+  BAM: path to BAM/SAM/CRAM alignment file
+
+Options:
+  --version              Show the version and exit.
+  -w, --wlen INTEGER     Window length for damage modeling  [default: 20]
+  -p, --process INTEGER  Number of processes  [default: 2]
+  -m, --mini INTEGER     Minimum reads aligned to consider reference
+                         [default: 2000]
+
+  -c, --cov FLOAT        Minimum coverage to consider reference  [default:
+                         0.5]
+
+  -s, --show_al          Show alignments representations
+  -pl, --plot            Make the damage plots
+  --verbose              Verbose mode
+  -o, --outdir PATH      Output directory  [default: pydamage_results]
+  --force                Force overwriting of results directory
+  --help                 Show this message and exit.
+```

docs/source/conf.py

@@ -10,9 +10,9 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
-# import os
-# import sys
-# sys.path.insert(0, os.path.abspath('.'))
+import os
+import sys
+sys.path.insert(0, os.path.abspath('../..'))
 
 source_parsers = {
     '.md': 'recommonmark.parser.CommonMarkParser',

docs/source/index.rst

@@ -15,6 +15,9 @@ __ homepage_
    :maxdepth: 2
    :caption: Contents:
 
+   API
+   CLI
+
 
 
 Indices and tables