diff --git a/docs/content/images/tool-glyphs/window-glyph.png b/docs/content/images/tool-glyphs/window-glyph.png
new file mode 100644
index 0000000000000000000000000000000000000000..38e0cf50ff92eeedc0e8eafcd6c2aedb706f0f1b
Binary files /dev/null and b/docs/content/images/tool-glyphs/window-glyph.png differ
diff --git a/docs/content/tools/window.rst b/docs/content/tools/window.rst
index 3c0c43112923fb292b30b683d8bbd379235b4ce0..496a93416c890544bedbb7ddaf86d476b5ce667e 100755
--- a/docs/content/tools/window.rst
+++ b/docs/content/tools/window.rst
@@ -2,156 +2,207 @@
*window*
###############
-Similar to **intersectBed**, **windowBed** searches for overlapping features in A and B. However,
-**windowBed** adds a specified number (1000, by default) of base pairs upstream and downstream of
-each feature in A. In effect, this allows features in B that are "near" features in A to be detected.
+|
-==========================================================================
+.. image:: ../images/tool-glyphs/window-glyph.png
+ :width: 600pt
+
+|
+
+Similar to ``bedtools intersect``, ``window`` searches for overlapping features
+in A and B. However, ``window`` adds a specified number (1000, by default) of
+base pairs upstream and downstream of each feature in A. In effect, this allows
+features in B that are "near" features in A to be detected.
+
+===============================
Usage and option summary
-==========================================================================
-**Usage:**
+===============================
+**Usage**:
::
- windowBed [OPTIONS] -a <BED/GFF/VCF> -b <BED/GFF/VCF>
+
+ bedtools window [OPTIONS] [-a|-abam] -b <BED/GFF/VCF>
+
+**(or)**:
+::
+
+ bedtools window [OPTIONS] [-a|-abam] -b <BED/GFF/VCF>
+
=========================== =========================================================================================================================================================
Option Description
=========================== =========================================================================================================================================================
-**-abam** BAM file A. Each BAM alignment in A is compared to B in search of overlaps. Use "stdin" if passing A with a UNIX pipe: For example: samtools view -b <BAM> | windowBed -abam stdin -b genes.bed
+**-abam** BAM file A. Each BAM alignment in A is compared to B in search of overlaps. Use "stdin" if passing A with a UNIX pipe: For example: samtools view -b <BAM> | bedtools window -abam stdin -b genes.bed
**-ubam** Write uncompressed BAM output. The default is write compressed BAM output.
-**-bed** When using BAM input (-abam), write output as BED. The default is to write output in BAM when using -abam. For example: windowBed -abam reads.bam -b genes.bed -bed
+**-bed** When using BAM input (-abam), write output as BED. The default is to write output in BAM when using -abam. For example: bedtools window -abam reads.bam -b genes.bed -bed
**-w** Base pairs added upstream and downstream of each entry in A when searching for overlaps in B. *Default is 1000 bp*.
**-l** Base pairs added upstream (left of) of each entry in A when searching for overlaps in B. *Allows one to create assymetrical "windows". Default is 1000bp*.
**-r** Base pairs added downstream (right of) of each entry in A when searching for overlaps in B. *Allows one to create assymetrical "windows". Default is 1000bp*.
**-sw** Define -l and -r based on strand. For example if used, -l 500 for a negative-stranded feature will add 500 bp downstream. *By default, this is disabled*.
**-sm** Only report hits in B that overlap A on the same strand. *By default, overlaps are reported without respect to strand*.
+**-Sm** Only report hits in B that overlap A on the same strand. *By default, overlaps are reported without respect to strand*.
**-u** Write original A entry once if any overlaps found in B. In other words, just report the fact at least one overlap was found in B.
**-c** For each entry in A, report the number of hits in B while restricting to -f. Reports 0 for A entries that have no overlap with B.
+**-v** Only report those entries in A that have *no overlaps* with B.
+**-header** Print the header from the A file prior to results.
=========================== =========================================================================================================================================================
+
==========================================================================
Default behavior
==========================================================================
-By default, **windowBed** adds 1000 bp upstream and downstream of each A feature and searches for
-features in B that overlap this "window". If an overlap is found in B, both the *original* A feature and the
-*original* B feature are reported. For example, in the figure below, feature B1 would be found, but B2
-would not.
-::
- Chromosome ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- "window" = 10
- BED File A <----------*************---------->
-
- BED File B ^^^^^^^^ ^^^^^^
-
- Result ========
-
-For example:
-::
- cat A.bed
+By default, ``bedtools window`` adds 1000 bp upstream and downstream of each A
+feature and searches for features in B that overlap this "window". If an overlap
+is found in B, both the *original* A feature and the *original* B feature are
+reported.
+
+.. code-block:: bash
+
+ $ cat A.bed
chr1 100 200
- cat B.bed
+ $ cat B.bed
chr1 500 1000
chr1 1300 2000
- windowBed -a A.bed -b B.bed
+ $ bedtools window -a A.bed -b B.bed
chr1 100 200 chr1 500 1000
==========================================================================
``-w`` Defining a custom window size
==========================================================================
-Instead of using the default window size of 1000bp, one can define a custom, *symmetric* window around
-each feature in A using the **-w** option. One should specify the window size in base pairs. For example,
-a window of 5kb should be defined as **-w 5000**.
+Instead of using the default window size of 1000bp, one can define a custom,
+*symmetric* window around each feature in A using the **-w** option. One should
+specify the window size in base pairs. For example, a window of 5kb should be
+defined as ``-w 5000``.
-For example (note that in contrast to the default behavior, the second B entry is reported):
-::
- cat A.bed
+For example (note that in contrast to the default behavior,
+the second B entry is reported):
+
+.. code-block:: bash
+
+ $ cat A.bed
chr1 100 200
- cat B.bed
+ $ cat B.bed
chr1 500 1000
chr1 1300 2000
- windowBed -a A.bed -b B.bed -w 5000
+ $ bedtools window -a A.bed -b B.bed -w 5000
chr1 100 200 chr1 500 1000
chr1 100 200 chr1 1300 2000
+
==========================================================================
-``-l and -r`` Defining assymteric windows
+``-l and -r`` Defining *assymteric* windows
==========================================================================
-One can also define asymmetric windows where a differing number of bases are added upstream and
-downstream of each feature using the **-l (upstream)** and **-r (downstream)** options.
+One can also define asymmetric windows where a differing number of bases are
+added upstream and downstream of each feature using the ``-l`` (upstream)
+and ``-r`` (downstream)** options.
+
+.. note::
+ By default, the ``-l`` and ``-r`` options ignore. If you want to define
+ *upstream* and *downstream* based on strand, use the ``-sw`` option (below)
+ with the ``-l`` and ``-r`` options.
+
For example (note the difference between -l 200 and -l 300):
-::
- cat A.bed
+
+
+.. code-block:: bash
+
+ $ cat A.bed
chr1 1000 2000
- cat B.bed
+ $ cat B.bed
chr1 500 800
chr1 10000 20000
- windowBed -a A.bed -b B.bed -l 200 -r 20000
+ $ bedtools window -a A.bed -b B.bed -l 200 -r 20000
chr1 100 200 chr1 10000 20000
- windowBed -a A.bed -b B.bed -l 300 -r 20000
+ $ bedtools window -a A.bed -b B.bed -l 300 -r 20000
chr1 100 200 chr1 500 800
chr1 100 200 chr1 10000 20000
+
==========================================================================
``-sw`` Defining assymteric windows based on strand
==========================================================================
-Especially when dealing with gene annotations or RNA-seq experiments, you may want to define
-asymmetric windows based on "strand". For example, you may want to screen for overlaps that occur
-within 5000 bp upstream of a gene (e.g. a promoter region) while screening only 1000 bp downstream of
-the gene. By enabling the **-sw** ("stranded" windows) option, the windows are added upstream or
-downstream according to strand. For example, imagine one specifies **-l 5000 -r 1000** as well as the **-
-sw** option. In this case, forward stranded ("+") features will screen 5000 bp to the *left* (that is, *lower*
-genomic coordinates) and 1000 bp to the *right* (that is, *higher* genomic coordinates). By contrast,
-reverse stranded ("-") features will screen 5000 bp to the *right* (that is, *higher* genomic coordinates) and
-1000 bp to the *left* (that is, *lower* genomic coordinates).
+Especially when dealing with gene annotations or RNA-seq experiments, you may
+want to define asymmetric windows based on "strand". For example, you may want
+to screen for overlaps that occur within 5000 bp upstream of a gene (e.g. a
+promoter region) while screening only 1000 bp downstream of the gene.
+By enabling the ``-sw`` ("stranded" windows) option, the windows are added
+upstream or downstream according to strand. For example, imagine one
+specifies ``-l 5000``, ``-r 1000`` as well as the ``-sw`` option. In this case,
+forward stranded ("+") features will screen 5000 bp to the *left* (that is,
+*lower* genomic coordinates) and 1000 bp to the *right* (that is, *higher*
+genomic coordinates). By contrast, reverse stranded ("-") features will screen
+5000 bp to the *right* (that is, *higher* genomic coordinates) and 1000 bp to
+the *left* (that is, *lower* genomic coordinates).
-For example (note the difference between -l 200 and -l 300):
-::
- cat A.bed
+For example (note the difference between ``-l 200`` and ``-l 300``):
+
+.. code-block:: bash
+
+ $ cat A.bed
chr1 10000 20000 A.forward 1 +
chr1 10000 20000 A.reverse 1 -
- cat B.bed
+ $ cat B.bed
chr1 1000 8000 B1
chr1 24000 32000 B2
- windowBed -a A.bed -b B.bed -l 5000 -r 1000 -sw
+ $ bedtools window -a A.bed -b B.bed -l 5000 -r 1000 -sw
chr1 10000 20000 A.forward 1 + chr1 1000 8000 B1
chr1 10000 20000 A.reverse 1 - chr1 24000 32000 B2
==========================================================================
-``-sm`` Enforcing "strandedness"
+``-sm`` Enforcing matches with the *same* "strandedness"
+==========================================================================
+This option behaves the same as the ``-s`` option for ``bedtools intersect``
+while scanning for overlaps within the "window" surrounding A. That is, overlaps
+in B will only be included if the B interval is on the *same* strand as the A
+interval.
+
+==========================================================================
+``-Sm`` Enforcing matches with the *same* "strandedness"
==========================================================================
-This option behaves the same as the -s option for intersectBed while scanning for overlaps within the
-"window" surrounding A. See the discussion in the intersectBed section for details.
+This option behaves the same as the ``-S`` option for ``bedtools intersect`` while
+scanning for overlaps within the "window" surrounding A. That is, overlaps in
+B will only be included if the B interval is on the *opposite* strand as the A
+interval.
+
==========================================================================
-``-u`` Reporting the presence of at least one overlapping feature
+``-u`` Reporting the presence/absence of at least one overlapping feature
==========================================================================
-This option behaves the same as for intersectBed while scanning for overlaps within the "window"
-surrounding A. See the discussion in the intersectBed section for details.
+This option behaves the same as for ``bedtools intersect``. That is, even if
+multiple overlaps exist, each A interval will only be reported once.
==========================================================================
``-c`` Reporting the number of overlapping features
==========================================================================
-This option behaves the same as for intersectBed while scanning for overlaps within the "window"
-surrounding A. See the discussion in the intersectBed section for details.
+This option behaves the same as for ``bedtools intersect``. That is, it will
+report the *count* of intervals in B that overlap each A interval.
+
==========================================================================
``-v`` Reporting the absence of any overlapping features
==========================================================================
-This option behaves the same as for intersectBed while scanning for overlaps within the "window"
-surrounding A. See the discussion in the intersectBed section for details.
+This option behaves the same as for ``bedtools intersect``. That is, it will
+only report those intervals in A that have have *zero* overlaps in B.
+
+==========================================================================
+``-header`` Print the header for the A file before reporting results.
+==========================================================================
+By default, if your A file has a header, it is ignored when reporting results.
+This option will instead tell bedtools to first print the header for the
+A file prior to reporting results.