@@ -83,19 +83,19 @@
diff --git a/docs/_build/html/searchindex.js b/docs/_build/html/searchindex.js
index ff6b65f..edccd69 100644
--- a/docs/_build/html/searchindex.js
+++ b/docs/_build/html/searchindex.js
@@ -1 +1 @@
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\ No newline at end of file
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9. Base track (
-draw base,
-bamplot base)","
11. Coordinates track (
-draw coordinates)","
8. Coverage track (
-bamplot coverage)","
2. Gallary","
10. Gene track (
-draw gene)","
12. Heatmap track (
-bamplot heatmap)","BamSnap","
4. Input files","
1. Installation","
3. Optional arguments","
5. Output files","
6. Plot options","
7. Read alignment track (
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\ No newline at end of file
diff --git a/docs/conf.py b/docs/conf.py
index 110008e..062a9d9 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -61,4 +61,20 @@
# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
\ No newline at end of file
+html_static_path = ['_static']
+
+html_theme_options = {
+ 'canonical_url': '',
+ 'logo_only': False,
+ 'display_version': True,
+ 'prev_next_buttons_location': 'bottom',
+ 'style_external_links': False,
+ 'vcs_pageview_mode': '',
+ 'style_nav_header_background': 'black',
+ # Toc options
+ 'collapse_navigation': True,
+ 'sticky_navigation': True,
+ 'navigation_depth': 4,
+ 'includehidden': True,
+ 'titles_only': False
+}
\ No newline at end of file
diff --git a/docs/index.rst b/docs/index.rst
index 1d505e4..4e06f8b 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -6,6 +6,18 @@
BamSnap
=======
+.. image:: https://img.shields.io/pypi/v/bamsnap.svg
+ :target: https://pypi.org/project/bamsnap/
+ :alt: Latest PyPI version
+
+.. image:: https://img.shields.io/pypi/dm/bamsnap.svg
+ :target: https://pypi.org/project/bamsnap/
+ :alt: Number of PyPI downloads
+
+.. image:: https://readthedocs.org/projects/bamsnap/badge/?version=latest
+ :target: https://bamsnap.readthedocs.io/en/latest/
+ :alt: Documentation of BamSnap
+
**BamSnap** is a high-performance visualization tool for aligned BAM file. **BamSnap** is a command line program written in python. All commands involve typing ``bamsnap`` at the command prompt (e.g. DOS window or Unix termninal) followed by a number of options to specify the data files / parameters to be used.
.. image:: ../tests/out/NATRIO_chr10_117542948.png
@@ -33,22 +45,13 @@ You can find more examples and commands in `gallary
`_. Use ``-h``
BamSnap is open-source and can be found on `github `_.
-.. image:: https://img.shields.io/pypi/v/bamsnap.svg
- :target: https://pypi.org/project/bamsnap/
- :alt: Latest PyPI version
-.. image:: https://img.shields.io/pypi/dm/bamsnap.svg
- :target: https://pypi.org/project/bamsnap/
- :alt: Number of PyPI downloads
-
-.. image:: https://readthedocs.org/projects/bamsnap/badge/?version=latest
- :target: https://bamsnap.readthedocs.io/en/latest/
- :alt: Documentation of BamSnap
Contents
--------
.. toctree::
+ :numbered:
:maxdepth: 4
installation.rst
diff --git a/docs/read_plot.rst b/docs/read_plot.rst
index 0a4bed1..f353845 100644
--- a/docs/read_plot.rst
+++ b/docs/read_plot.rst
@@ -17,19 +17,6 @@ Layout options
* ``-no_target_line`` (default=false): do not draw target line
-.. code:: console
-
- $ bamsnap \
- -bam ./data/NA12879.bam \
- -pos chr10:117542948 \
- -no_title \
- -draw bamplot \
- -bamplot read \
- -out ./out/NATRIO_chr10_117542948_3.png \
- -read_thickness 15 \
- -read_gap_height 10 \
- -read_gap_width 5
-
Read group (``-read_group``)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -39,16 +26,18 @@ Read group (``-read_group``)
* ``-read_pos_color`` (default='FFAC9C') : positive strand read color
* ``-read_neg_color`` (default='A19CFF') : negative strand read color
-.. code:: console
-
- $ bamsnap \
- -bam ./data/NA12879.bam \
- -pos chr10:117542948 \
- -no_title \
- -draw bamplot \
- -bamplot read \
- -out ./out/NATRIO_chr10_117542948_6.png \
- -read_group strand
+.. code-block:: console
+ :linenos:
+ :emphasize-lines: 6,8
+
+ $ bamsnap \
+ -bam ./data/NA12879.bam \
+ -pos chr10:117542948 \
+ -no_title \
+ -draw bamplot \
+ -bamplot read \
+ -out ./out/NATRIO_chr10_117542948_6.png \
+ -read_group strand
.. image:: ../tests/out/NATRIO_chr10_117542948_6.png
:width: 100 %