diff --git a/docs/content/tools/shuffle.rst b/docs/content/tools/shuffle.rst index 26d3716f7d8c65df82b90ec1590a3d53339b12f6..8ad9fba1590a7defaf5de30cbbb789c9525279cc 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 cea9e4d5e85cbf77f3031970a6644be292fd15dd..5acbef8855e2ffb9695b39d7127e718c8e8174bc 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;