use Getopt::Long;
use Pod::Usage;
use File::Basename;
-use Switch;
use strict;
#const
my $strand_specific = 0;
+my $version = 0;
+
my $mTime = 0;
my ($time_start, $time_end, $time_alignment, $time_rsem, $time_ci) = (0, 0, 0, 0, 0);
"calc-ci" => \$calcCI,
"ci-memory=i" => \$NMB,
"time" => \$mTime,
+ "version" => \$version,
"q|quiet" => \$quiet,
"h|help" => \$help) or pod2usage(-exitval => 2, -verbose => 2);
-pod2usage(-verbose => 2) if ($help == 1);
+my ($fn, $dir, $suf) = fileparse($0);
+pod2usage(-verbose => 2) if ($help == 1);
+&showVersionInfo($dir) if ($version == 1);
#check parameters and options
if ($bowtie_path ne "") { $bowtie_path .= "/"; }
-my ($fn, $dir, $suf) = fileparse($0);
my $command = "";
if (!$is_sam && !$is_bam) {
&runCommand($command);
$command = $dir."rsem-build-read-index $gap";
-switch($read_type) {
- case 0 { $command .= " 0 $quiet $imdName\_alignable.fa"; }
- case 1 { $command .= " 1 $quiet $imdName\_alignable.fq"; }
- case 2 { $command .= " 0 $quiet $imdName\_alignable_1.fa $imdName\_alignable_2.fa"; }
- case 3 { $command .= " 1 $quiet $imdName\_alignable_1.fq $imdName\_alignable_2.fq"; }
-}
+if ($read_type == 0) { $command .= " 0 $quiet $imdName\_alignable.fa"; }
+elsif ($read_type == 1) { $command .= " 1 $quiet $imdName\_alignable.fq"; }
+elsif ($read_type == 2) { $command .= " 0 $quiet $imdName\_alignable_1.fa $imdName\_alignable_2.fa"; }
+elsif ($read_type == 3) { $command .= " 1 $quiet $imdName\_alignable_1.fq $imdName\_alignable_2.fq"; }
+else { print "Impossible! read_type is not in [1,2,3,4]!\n"; exit(-1); }
&runCommand($command);
my $doesOpen = open(OUTPUT, ">$imdName.mparams");
if ($status != 0) {
my $errmsg = "";
if (scalar(@_) > 1) { $errmsg .= $_[1]."\n"; }
- $errmsg .= "\"$_[0]\" failed! Plase check if you provide correct parameters/options for the pipeline!\n";
+ $errmsg .= "\"$_[0]\" failed! Please check if you provide correct parameters/options for the pipeline!\n";
print $errmsg;
exit(-1);
}
close(OUTPUT);
}
+# dir
+sub showVersionInfo {
+ open(INPUT, "$_[0]\WHAT_IS_NEW");
+ my $line = <INPUT>;
+ chomp($line);
+ close(INPUT);
+ print "$line\n";
+ exit(0);
+}
+
__END__
=head1 NAME