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#!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
my $usage = "usage: $0 reads.fasta ref_transcripts.fasta [SS]\n\n";
my $reads_file = $ARGV[0] or die $usage;
my $ref_transcripts_fasta = $ARGV[1] or die $usage;
my $SS_flag = $ARGV[2] || 0;
my $cmd = "$FindBin::RealBin/../../Inchworm/bin/inchworm "
. " --reads $reads_file "
. " --checkFastaPath $ref_transcripts_fasta ";
unless ($SS_flag) {
$cmd .= " --DS ";
}
my $ret = system($cmd);
if ($ret) {
die "Error, CMD: $cmd died with ret $ret";
}
exit(0);
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