#!/usr/bin/perl

use Getopt::Long;
use Pod::Usage;
use File::Basename;
use strict;

my $gene_list = 0; # default is 0, means input is a transcript list; 1 means input is a gene list
my $show_unique = 0; # 0, default value, means do not show unique transcript wiggles; 1 means show unique transcript wiggles
my $help = 0;

GetOptions("gene-list" => \$gene_list,
	   "show-unique" => \$show_unique,
	   "h|help" => \$help) or pod2usage(-exitval => 2, -verbose => 2);

pod2usage(-verbose => 2) if ($help == 1);
pod2usage(-msg => "Invalid number of arguments!", -exitval => 2, -verbose => 2) if (scalar(@ARGV) != 3);

my ($fn, $dir, $suf) = fileparse($0);
my $command = "";

unless (-e "$ARGV[0].transcript.readdepth") {
    $command = $dir."rsem-bam2readdepth $ARGV[0].transcript.sorted.bam > $ARGV[0].transcript.readdepth";
    &runCommand($command);
}

if ($show_unique) {
    unless (-e "$ARGV[0].uniq.transcript.bam") {
	$command = $dir."rsem-get-unique $ARGV[0].transcript.bam $ARGV[0].uniq.transcript.bam";
	&runCommand($command);
    }
    unless (-e "$ARGV[0].uniq.transcript.sorted.bam") {
	$command = $dir."sam/samtools sort $ARGV[0].uniq.transcript.bam $ARGV[0].uniq.transcript.sorted";
	&runCommand($command);
    }
    unless (-e "$ARGV[0].uniq.transcript.readdepth") {
	$command = $dir."rsem-bam2readdepth $ARGV[0].uniq.transcript.sorted.bam > $ARGV[0].uniq.transcript.readdepth";
	&runCommand($command);
    }
}

$command = $dir."rsem-gen-transcript-plots $ARGV[0] $ARGV[1] $gene_list $show_unique $ARGV[2]";
&runCommand($command);

# command, {err_msg}
sub runCommand {
    print $_[0]."\n";
    my $status = system($_[0]);
    if ($status != 0) { 
	my $errmsg;
	if (scalar(@_) > 1) { $errmsg = $_[1]; }
	else { $errmsg = "\"$command\" failed! Plase check if you provide correct parameters/options for the pipeline!"; }
	print $errmsg."\n";
	exit(-1);
    }
    print "\n";
}

__END__

=head1 NAME

rsem-plot-transcript-wiggles

=head1 SYNOPSIS

=over

 rsem-plot-transcript-wiggles [options] sample_name input_list output_plot_file

=back

=head1 ARGUMENTS

=over

=item B<sample_name>

The name of the sample analyzed.

=item B<input_list>

A list of transcript ids or gene ids. But it cannot be a mixture of transcript & gene ids.

=item B<output_plot_file>

The file name for the plots.

=back

=head1 OPTIONS

=over

=item B<--gene-list>

The input-list is a list of gene ids. (Default: off)

=item B<--show-unique>

Show unique wiggle. (Default: off)

=item B<-h/--help>

Show help information.

=back

=head1 DESCRIPTION

blablabla

=head1 OUTPUT

blablabla

=head1 EXAMPLES

blablabla

=cut