Skip to content

Commit

Permalink
Update documentation
Browse files Browse the repository at this point in the history
  • Loading branch information
alexpreynolds committed Feb 26, 2017
1 parent c00fabc commit 96b1e66
Show file tree
Hide file tree
Showing 3 changed files with 20 additions and 2 deletions.
2 changes: 1 addition & 1 deletion docs/conf.py
Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,7 @@

# General information about the project.
project = u'BEDOPS'
copyright = u'2011-2016, Shane Neph, Alex Reynolds'
copyright = u'2011-2017, Shane Neph, Alex Reynolds'

# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
Expand Down
17 changes: 17 additions & 0 deletions docs/content/summary.rst
Original file line number Diff line number Diff line change
Expand Up @@ -365,6 +365,23 @@ Compression and extraction
| ``--report-progress=N`` | Write progress to standard error stream for every N input elements. | 1 | No imposed limit | NA |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+

---------------
``starchstrip``
---------------

* Extract or filter a ``starch`` archive by one or more specified chromosome names.
* BEDOPS :ref:`starchstrip <starchstrip>` documentation.

+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| option | description | min. file inputs | max. file inputs | min. BED columns |
+===============================+======================================================================+==================+==================+==================+
| (no option) | NA | 1 | No imposed limit | NA |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+
| ``--include`` or ``--exclude``| Writes output with inclusion or exclusion of specified chromosome | NA | No imposed limit | NA |
| with <chromosomes> | name records (comma-delimited string). | | | |
+-------------------------------+----------------------------------------------------------------------+------------------+------------------+------------------+


.. |--| unicode:: U+2013 .. en dash
.. |---| unicode:: U+2014 .. em dash, trimming surrounding whitespace
:trim:
3 changes: 2 additions & 1 deletion docs/index.rst
Original file line number Diff line number Diff line change
Expand Up @@ -154,6 +154,7 @@ Contents
<li><a href="content/reference/file-management/sorting/sort-bed.html"><tt>sort-bed</tt></a> - apply lexicographical sort to BED data</li>
<li><a href="content/reference/file-management/compression/starch.html"><tt>starch</tt></a> and <a href="content/reference/file-management/compression/unstarch.html"><tt>unstarch</tt></a> - compress and extract BED data</li>
<li><a href="content/reference/file-management/compression/starchcat.html"><tt>starchcat</tt></a> - merge compressed archives</li>
<li><a href="content/reference/file-management/compression/starchstrip.html"><tt>starchstrip</tt></a> - filter archive by chromosomes</li>
<li><a href="content/reference/file-management/conversion.html">Conversion tools</a> - convert common genomic formats to BED</li>
</ul>
</div>
Expand Down Expand Up @@ -238,7 +239,7 @@ Contents
<li><a href="content/reference/file-management/sorting/sort-bed.html"><tt>sort-bed</tt></a> - apply lexicographical sort to BED data</li>
<li><a href="content/reference/file-management/compression/starch.html"><tt>starch</tt></a> and <a href="content/reference/file-management/compression/unstarch.html"><tt>unstarch</tt></a> - compress and extract BED data</li>
<li><a href="content/reference/file-management/compression/starchcat.html"><tt>starchcat</tt></a> - merge compressed archives</li>
<li><a href="content/reference/file-management/compression/starchsplit.html"><tt>starchsplit</tt></a> - filter archives by chromosome names</li>
<li><a href="content/reference/file-management/compression/starchstrip.html"><tt>starchstrip</tt></a> - filter archives by chromosome names</li>
<li><a href="content/reference/file-management/conversion.html">Conversion tools</a> - convert common genomic formats to BED</li>
</ul>

Expand Down

0 comments on commit 96b1e66

Please sign in to comment.