sync docs

docs/content/tips-and-tricks.rst

 ###############
 Tips and Tricks
-###############
\ No newline at end of file
+###############
+
+======================
+The ``-sorted`` option
+======================
\ No newline at end of file

docs/content/tools/bamtobed.rst

@@ -38,9 +38,11 @@ Option          Description
                 always report mate one as the first BEDPE "block".		 
 **-bed12**      Write "blocked" BED (a.k.a. BED12) format. This will convert 
                 "spliced" BAM alignments (denoted by the "N" CIGAR operation) 
-                to BED12.
+                to BED12. `Forces -split`.
 **-split**      Report each portion of a "split" BAM (i.e., having an "N" CIGAR 
                 operation) alignment as a distinct BED intervals.
+**-splitD**     Report each portion of a "split" BAM while obeying noth "N" CIGAR 
+                and "D" operation. Forces `-split`.
 **-ed**         Use the "edit distance" tag (NM) for the BED score field. 
                 Default for BED is to use mapping quality. Default for BEDPE is 
                 to use the *minimum* of the two mapping qualities for the pair. 

docs/content/tools/flank.rst

@@ -119,7 +119,7 @@ For example:
   # are 20bp whereas the flanking intervals from the first record
   # are only 10bp
   ################################################################
-  $ bedtools flank -i A.bed -g my.genome -b 0.5 -pct
+  $ bedtools flank -i A.bed -g my.genome -b 0.1 -pct
   chr1	90	100
   chr1	200	210
   chr1	480	500

docs/content/tools/intersect.rst

@@ -21,7 +21,7 @@ with both BED/GFF/VCF and BAM files as input.
 
     If you are trying to intersect very large files and are having trouble
     with excessive memory usage, please presort your data by chromosome and
-    then by start position (e.g., ``sort k1,1 -k2,2n in.bed > in.sorted.bed``
+    then by start position (e.g., ``sort -k1,1 -k2,2n in.bed > in.sorted.bed``
     for BED files) and then use the ``-sorted`` option.  This invokes a 
     memory-efficient algorithm designed for large files.
 

docs/content/tools/shuffle.rst

@@ -48,6 +48,7 @@ Usage and option summary
 **-bedpe**	                     Indicate that the A file is in BEDPE format.
 **-maxTries**                    Max. number of attempts to find a home for a shuffled interval in the presence of -incl or -excl. *Default = 1000.*
 **-noOverlapping**               Don't allow shuffled intervals to overlap.
+**-allowBeyondChromEnd**         Allow the original the length of the original records to extebd beyond the length of the chromosome.
 ===========================      ===============================================================================================================================================================================================================
 
 
@@ -207,4 +208,23 @@ no such overlaps.
   $ bedtools shuffle -i A.bed -g my.genome -noOverlapping
 
 
+==========================================================================
+``-allowBeyondChromEnd`` Allow records to extend beyond the chrom. length.
+==========================================================================
+By default, ``shuffle`` requires that an interval's original length must be 
+fully-contained within the chromosome. Yet there are cases where you might 
+want to allow shuffled intervals to be relocated to a position
+in which the entire original interval cannot fit w/o exceeding
+the end of the chromosome.  By using the ``-noOverlapping`` option, 
+``shuffle`` will allow intervals to be shuffled to locations that are so close
+to the chromosome end that the full length of the original record cannot
+be contained within the chromosome length.  In such cases, the end coordinate
+for the shuffled interval will be set (i.e., truncated) 
+to the chromosome's length.
+
+.. code-block:: bash
+
+  $ bedtools shuffle -i A.bed -g my.genome -allowBeyondChromEnd
+
+
 

docs/content/tools/window.rst

@@ -103,7 +103,7 @@ and ``-r`` (downstream)** options.
 
 .. note::
 
-    By default, the ``-l`` and ``-r`` options ignore.  If you want to define
+    By default, the ``-l`` and ``-r`` options ignore strand.  If you want to define
     *upstream* and *downstream* based on strand, use the ``-sw`` option (below)
     with the ``-l`` and ``-r`` options.
     

docs/themes/rtd/static/rtd.css_t

@@ -525,6 +525,9 @@ div.warning p.admonition-title {
 }
 
 
+
+
+
 /* Sidebars only */
 div.sidebar {
   max-width: 200px;