diff --git a/README.md b/README.md
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/data/aluY.hg19.bed.gz b/data/aluY.hg19.bed.gz
deleted file mode 100644
index 80c462579972331c8dd3cfd9cb8e03c27caa574e..0000000000000000000000000000000000000000
Binary files a/data/aluY.hg19.bed.gz and /dev/null differ
diff --git a/docs/content/tips-and-tricks.rst b/docs/content/tips-and-tricks.rst
index 28b149b7bb7a538c01f9d98714ba9c5def3f1420..61f35984279bd70f501baf85a3eed4474257b5a0 100644
--- a/docs/content/tips-and-tricks.rst
+++ b/docs/content/tips-and-tricks.rst
@@ -1,3 +1,7 @@
###############
Tips and Tricks
-###############
\ No newline at end of file
+###############
+
+======================
+The ``-sorted`` option
+======================
\ No newline at end of file
diff --git a/docs/content/tools/bamtobed.rst b/docs/content/tools/bamtobed.rst
index 5c0506dbf627c116db54f63783767ad15f70a3c7..f075bb56cd38712da9c5f11389efcee9c9b30e2b 100755
--- a/docs/content/tools/bamtobed.rst
+++ b/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.
diff --git a/docs/content/tools/flank.rst b/docs/content/tools/flank.rst
index c952eaf87e2f1f8c780f58be837de34b4d7d6937..a210ef69b6beca113b42e1b702cdde0621c430ff 100644
--- a/docs/content/tools/flank.rst
+++ b/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
diff --git a/docs/content/tools/intersect.rst b/docs/content/tools/intersect.rst
index 0aa8fa9747d15be1a5f6cdfe1874a464daf5c1e7..f4dc92dc8cf277a6c2db1c0b055570ee9991271d 100755
--- a/docs/content/tools/intersect.rst
+++ b/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.
diff --git a/docs/content/tools/shuffle.rst b/docs/content/tools/shuffle.rst
index 8ad9fba1590a7defaf5de30cbbb789c9525279cc..0bde195463cc62eede860c1f7e219f614324f465 100755
--- a/docs/content/tools/shuffle.rst
+++ b/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
+
+
diff --git a/docs/content/tools/window.rst b/docs/content/tools/window.rst
index 496a93416c890544bedbb7ddaf86d476b5ce667e..df7f6858bc733fe9d57ba1ba46462c888a5c2b2d 100755
--- a/docs/content/tools/window.rst
+++ b/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.
diff --git a/docs/themes/rtd/static/rtd.css_t b/docs/themes/rtd/static/rtd.css_t
index 66736c00c58c8df78930cce4948ecf2deb6dc0d2..4302d930d7e4f3f413e841d3e2768af2e3c0c42b 100755
--- a/docs/themes/rtd/static/rtd.css_t
+++ b/docs/themes/rtd/static/rtd.css_t
@@ -525,6 +525,9 @@ div.warning p.admonition-title {
}
+
+
+
/* Sidebars only */
div.sidebar {
max-width: 200px;