[DOC] update docs for merge and cluster

docs/content/tools/cluster.rst

 ###############
 *cluster*
-###############
\ No newline at end of file
+###############
+
+|
+
+.. image:: ../images/tool-glyphs/cluster-glyph.png 
+    :width: 600pt 
+|
+
+
+Similar to :doc:`../tools/merge`, ``cluster`` report each set of overlapping or 
+"book-ended" features in an interval file.  In contrast to ``merge``, 
+``cluster`` does not flatten the cluster of intervals into a new meta-interval;
+instead, it assigns an unique cluster ID to each record in each cluster.  This
+is useful for having fine control over how sets of overlapping intervals in 
+a single interval file are combined.
+
+.. note::
+
+    ``bedtools cluster`` requires that you presort your data by chromosome and
+    then by start position (e.g., ``sort k1,1 -k2,2n in.bed > in.sorted.bed``
+    for BED files).
+    
+.. seealso::
+
+    :doc:`../tools/merge`
+    
+
+==========================================================================
+Usage and option summary
+==========================================================================
+**Usage**:
+::
+
+  bedtools cluster [OPTIONS] -i <BED/GFF/VCF> 
+
+**(or)**:
+::
+
+  clusterBed [OPTIONS] -i <BED/GFF/VCF>
+
+
+  
+===========================      ===============================================================================================================================================================================================================
+Option                           Description
+===========================      ===============================================================================================================================================================================================================
+**-s**				             Force strandedness. That is, only cluster features that are the same strand. *By default, this is disabled*.
+**-d**                           Maximum distance between features allowed for features to be clustered. *Default is 0. That is, overlapping and/or book-ended features are clustered*.
+===========================      ===============================================================================================================================================================================================================
+
+
+
+
+
+==========================================================================
+Default behavior
+==========================================================================
+By default, ``bedtools cluster`` collects overlapping (by at least 1 bp) and/or
+bookended intervals into distinct clusters.  In the example below, the 4th 
+column is the cluster ID.
+  
+.. code-block:: bash
+
+  $ cat A.bed
+  chr1  100  200
+  chr1  180  250
+  chr1  250  500
+  chr1  501  1000
+
+  $ bedtools cluster -i A.bed
+  chr1	100	200	1
+  chr1	180	250	1
+  chr1	250	500	1
+  chr1	501	1000	2
+
+
+==========================================================================
+``-s`` Enforcing "strandedness" 
+==========================================================================
+The ``-s`` option will only cluster intervals that are overlapping/bookended
+*and* are on the same strand.
+
+.. code-block:: bash
+
+  $ cat A.bed
+  chr1  100  200   a1  1 +
+  chr1  180  250   a2  2 +
+  chr1  250  500   a3  3 - 
+  chr1  501  1000  a4  4 +
+
+  $ bedtools cluster -i A.bed -s
+  chr1	100	200	a1	1	+	1
+  chr1	180	250	a2	2	+	1
+  chr1	501	1000	a4	4	+	2
+  chr1	250	500	a3	3	-	3
+
+
+==========================================================================
+``-d`` Controlling how close two features must be in order to cluster 
+==========================================================================
+By default, only overlapping or book-ended features are combined into a new 
+feature. However, one can force ``cluster`` to combine more distant features 
+with the ``-d`` option. For example, were one to set ``-d`` to 1000, any 
+features that overlap or are within 1000 base pairs of one another will be 
+clustered.
+
+.. code-block:: bash
+
+  $ cat A.bed
+  chr1  100  200
+  chr1  501  1000
+  
+  $ bedtools cluster -i A.bed
+  chr1  100  200    1
+  chr1  501  1000   2
+
+  $ bedtools cluster -i A.bed -d 1000
+  chr1  100  200    1
+  chr1  501  1000   1
+

docs/content/tools/merge.rst

@@ -34,7 +34,7 @@ Usage and option summary
 **(or)**:
 ::
 
-  mergeBed [OPTIONS] -i <BED/GFF/VCF> -g <GENOME>
+  mergeBed [OPTIONS] -i <BED/GFF/VCF>
 
 
   
@@ -89,7 +89,7 @@ The ``-s`` option will only merge intervals that are overlapping/bookended
   chr1  250  500   a3  3 - 
   chr1  501  1000  a4  4 +
 
-  $ bedtools merge -i A.bed
+  $ bedtools merge -i A.bed -s
   chr1  100  250    +
   chr1  501  1000   +
   chr1  250  500    -