From 79fa169d07c7a20e3e9598e6d32d99353383bd22 Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Tue, 13 Aug 2013 21:08:49 -0400
Subject: [PATCH] [DOC] add docs for the -noOverlapping option in shuffle.
---
docs/content/tools/shuffle.rst | 16 ++++++++++++++++
src/shuffleBed/shuffleBedMain.cpp | 2 +-
2 files changed, 17 insertions(+), 1 deletion(-)
diff --git a/docs/content/tools/shuffle.rst b/docs/content/tools/shuffle.rst
index 26d3716f..8ad9fba1 100755
--- a/docs/content/tools/shuffle.rst
+++ b/docs/content/tools/shuffle.rst
@@ -47,6 +47,7 @@ Usage and option summary
**-chromFirst** Instead of choosing a position randomly among the entire genome (the default), first choose a chrom randomly, and then choose a random start coordinate on that chrom. This leads to features being ~uniformly distributed among the chroms, as opposed to features being distribute as a function of chrom size.
**-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.
=========================== ===============================================================================================================================================================================================================
@@ -192,3 +193,18 @@ of the chromosome*):
$ bedtools shuffle -i A.bed -g my.genome -seed 927442958
chr1 6177 6277 a1 1 +
chr1 8119 9119 a2 2 -
+
+==========================================================================
+``-noOverlapping`` Prevent shuffled intervals from overlapping.
+==========================================================================
+There often arise cases where one wants to shuffle intervals throughout
+the genome, yet one wants to prevent the intervals from occupying a single
+common base pair. The ``-noOverlapping`` option allows one to enforce
+no such overlaps.
+
+.. code-block:: bash
+
+ $ bedtools shuffle -i A.bed -g my.genome -noOverlapping
+
+
+
diff --git a/src/shuffleBed/shuffleBedMain.cpp b/src/shuffleBed/shuffleBedMain.cpp
index cea9e4d5..5acbef88 100644
--- a/src/shuffleBed/shuffleBedMain.cpp
+++ b/src/shuffleBed/shuffleBedMain.cpp
@@ -198,7 +198,7 @@ void shuffle_help(void) {
cerr << "\t-maxTries\t" << "\n\t\tMax. number of attempts to find a home for a shuffled interval" << endl;
cerr << "\t\tin the presence of -incl or -excl." << endl;
cerr << "\t\tDefault = 1000." << endl;
- cerr << "\t-noOverlapping\t" << "\n\t\tdont allow shuffled intervals to overlap." << endl;
+ cerr << "\t-noOverlapping\t" << "\n\t\tDon't allow shuffled intervals to overlap." << endl;
cerr << "Notes: " << endl;
cerr << "\t(1) The genome file should tab delimited and structured as follows:" << endl;
--
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