From 7ff5a9291398e5a3053a6520724cf83a242b11ff Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Sat, 26 Jan 2013 14:42:21 -0500
Subject: [PATCH] [DOC] prefer :doc: directive for internal links
---
docs/content/tools/intersect.rst | 11 +++++++----
docs/content/tools/slop.rst | 7 ++++---
2 files changed, 11 insertions(+), 7 deletions(-)
diff --git a/docs/content/tools/intersect.rst b/docs/content/tools/intersect.rst
index aa6f625c..0aa8fa97 100755
--- a/docs/content/tools/intersect.rst
+++ b/docs/content/tools/intersect.rst
@@ -25,7 +25,11 @@ with both BED/GFF/VCF and BAM files as input.
for BED files) and then use the ``-sorted`` option. This invokes a
memory-efficient algorithm designed for large files.
+.. seealso::
+ :doc:`../tools/subtract`
+ :doc:`../tools/window`
+
===============================
Usage and option summary
===============================
@@ -38,8 +42,9 @@ Usage and option summary
::
intersectBed [OPTIONS] [-a|-abam] -b <BED/GFF/VCF>
-
-
+
+
+
=========================== =========================================================================================================================================================
Option Description
@@ -73,8 +78,6 @@ Default behavior
By default, if an overlap is found, ``bedtools intersect`` reports the shared interval between the two
overlapping features.
-For example:
-
.. code-block:: bash
$ cat A.bed
diff --git a/docs/content/tools/slop.rst b/docs/content/tools/slop.rst
index c6f265ee..4a748456 100755
--- a/docs/content/tools/slop.rst
+++ b/docs/content/tools/slop.rst
@@ -4,7 +4,7 @@
|
-.. image:: ../images/tool-glyphs/intersect-glyph.png
+.. image:: ../images/tool-glyphs/slop-glyph.png
:width: 600pt
|
@@ -31,6 +31,7 @@ Usage and option summary
bedtools slop [OPTIONS] -i <BED/GFF/VCF> -g <GENOME> [-b or (-l and -r)]
**(or):**
+::
bedtools slop [OPTIONS] -i <BED/GFF/VCF> -g <GENOME> [-b or (-l and -r)]
@@ -41,8 +42,8 @@ Usage and option summary
**-l** The number of base pairs to subtract from the start coordinate. *Integer*.
**-r** The number of base pairs to add to the end coordinate. *Integer*.
**-s** Define -l and -r based on strand. For example. if used, -l 500 for a negative-stranded feature, it will add 500 bp to the *end* coordinate.
-**-pct**
-**-header**
+**-pct** Define -l and -r as a fraction of the feature's length. E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp "upstream". Default = false.
+**-header** Print the header from the input file prior to results.
=========================== ===============================================================================================================================================================================================================
--
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