LICENSE
    strucVis : Display small RNA depth of coverage on a predicted RNA
    secondary structure

    Copyright (C) 2016-2018 Michael J. Axtell

    This program is free software: you can redistribute it and/or modify it
    under the terms of the GNU General Public License as published by the
    Free Software Foundation, either version 3 of the License, or (at your
    option) any later version.

        This program is distributed in the hope that it will be useful,
        but WITHOUT ANY WARRANTY; without even the implied warranty of
        MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
        GNU General Public License for more details.

        You should have received a copy of the GNU General Public License
        along with this program.  If not, see <http://www.gnu.org/licenses/>.

AUTHOR
    Michael J. Axtell, Penn State University [email protected]

REQUIREMENTS
    perl5 (installed at /usr/bin/perl)

    samtools (installed in your PATH)

    RNAfold (installed in your PATH)

USAGE
        strucVis -b [bam] -g [genome] -c [Chr:start-stop] -s [strand 'plus' or 'minus'] -p [output.ps] -n [Locus name]

INPUTS
    -b : path to sorted and indexed BAM alignment file of small RNAs

    -g : path to FASTA formatted reference genome. Must be indexed using
    samtools faidx.

    -c : Coordinates of interest in format Chr:start-stop.

    -s : Strand of interest. Either 'plus' or 'minus'.

    -p : Output postscript file name. Must end in .ps

    -n : Name of locus. Prints name in the .ps file and on the plain text
    alignments. If not provided, defaults to 'Unnamed Locus'

SWITCHES
    -x : Suppress the printing of detailed file information on the
    post-script file

    -v : Print the version and quit

    -h : Print help message and quit

OUTPUT
    The text-based output of RNAfold is sent to STDOUT along with a
    text-based 'read cloud' of all aligned reads. The annotated post-script
    file goes to the file indicated by -p.

CHANGELOG
  version 0.4 2018-06-19
    Added switch -x

  version 0.3 2017-09-06
    Added option -n

  version 0.2
    Added 'read cloud' print-out of all reads.

    Restricted input alignments to be used to only include primary
    alignments without indels, introns, clipping, or padding.

  version 0.1
    First release