[DOC] add docs for the jaccard tool.

docs/content/tools/jaccard.rst

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 *jaccard*
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+|
+
+.. image:: ../images/tool-glyphs/jaccard-glyph.png 
+    :width: 600pt 
+
+Whereas the bedtools ``intersect`` tool enumerates each an every intersection between two sets of genomic
+intervals, one often needs a single statistic reflecting the *similarity* of the two sets based on the
+intersections between them. The Jaccard statistic is used in set theory to represent the ratio of the 
+intersection of two sets to the union of the two sets. Similarly, Favorov et al [1] reported the use
+of the Jaccard statistic for genome intervals: specifically, it measures the ratio of the number of
+intersecting base pairs between two sets to the number of base pairs in the union of the two sets.
+The bedtools jaccard tool implements this statistic, yet modifies the statistic such that the length of the 
+intersection is subtracted from the length of the union. As a result, the final statistic ranges from 0.0
+to 1.0, where 0.0 represents no overlap and 1.0 represent complete overlap.
+
+.. code::
+
+    [1] Exploring Massive, Genome Scale Datasets with the GenometriCorr Package. 
+    Favorov A, Mularoni L, Cope LM, Medvedeva Y, Mironov AA, et al. (2012) 
+    PLoS Comput Biol 8(5): e1002529. doi:10.1371/journal.pcbi.1002529
+
+
+.. note::
+
+    The ``jaccard`` tool requires that your data is pre-sorted 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/reldist`
+    :doc:`../tools/intersect`
+    
+
+===============================
+Usage and option summary
+===============================
+**Usage**:
+::
+
+  bedtools jaccard [OPTIONS] -a <BED/GFF/VCF> -b <BED/GFF/VCF>
+
+
+===========================    =========================================================================================================================================================
+Option                         Description
+===========================    =========================================================================================================================================================
+**-a**                           BED/GFF/VCF file A. Each feature in A is compared to B in search of overlaps. Use "stdin" if passing A with a UNIX pipe.
+**-b**                           BED/GFF/VCF file B. Use "stdin" if passing B with a UNIX pipe.
+**-f**                           Minimum overlap required as a fraction of A. Default is 1E-9 (i.e. 1bp).
+**-r**                           Require that the fraction of overlap be reciprocal for A and B. In other words, if -f is 0.90 and -r is used, this requires that B overlap at least 90% of A and that A also overlaps at least 90% of B.
+===========================    =========================================================================================================================================================
+
+
+===============================
+Default behavior
+===============================
+By default, ``bedtools jaccard`` reports the length of the intersection, the length of the union (minus the intersection), 
+the final Jaccard statistic reflecting the similarity of the two sets, as well as the number of intersections.
+
+.. code-block:: bash
+
+  $ cat a.bed
+  chr1  10  20
+  chr1  30  40
+
+  $ cat b.bed
+  chr1  15   20
+
+  $ bedtools jaccard -a a.bed -b b.bed
+  intersection	union	jaccard	n_intersections
+  5	20	0.25	1
+
+============================================
+Controlling which intersections are included
+============================================
+One can also control which intersections are included in the statistic by requiring a certain fraction of overlap
+with respect to the features in A (via the ``-f`` parameter) or also by requiring that the fraction of overlap is
+reciprocal (``-r``) in A and B.
+
+.. code-block:: bash
+
+  $ cat a.bed
+  chr1  10  20
+  chr1  30  40
+
+  $ cat b.bed
+  chr1  15   20
+
+Require 10% overlap with respect to the intervals in A:
+
+.. code-block:: bash
+
+  $ bedtools jaccard -a a.bed -b b.bed -f 0.1
+  intersection  union   jaccard n_intersections
+  5 20  0.25    1
+
+Require 60% overlap with respect to the intervals in A:
+
+.. code-block:: bash
+
+  $ bedtools jaccard -a a.bed -b b.bed -f 0.6
+  intersection  union   jaccard n_intersections
+  0 25  0.25    0
+