my ($fn, $dir, $suf) = fileparse($0);
my $command = "";
+unless (-e "$ARGV[0].transcript.sorted.bam") {
+ $command = $dir."sam/samtools sort $ARGV[0].transcript.bam $ARGV[0].transcript.sorted";
+ &runCommand($command);
+}
unless (-e "$ARGV[0].transcript.readdepth") {
- $command = $dir."rsem-bam2readdepth $ARGV[0].transcript.sorted.bam > $ARGV[0].transcript.readdepth";
+ $command = $dir."rsem-bam2readdepth $ARGV[0].transcript.sorted.bam $ARGV[0].transcript.readdepth";
&runCommand($command);
}
&runCommand($command);
}
unless (-e "$ARGV[0].uniq.transcript.readdepth") {
- $command = $dir."rsem-bam2readdepth $ARGV[0].uniq.transcript.sorted.bam > $ARGV[0].uniq.transcript.readdepth";
+ $command = $dir."rsem-bam2readdepth $ARGV[0].uniq.transcript.sorted.bam $ARGV[0].uniq.transcript.readdepth";
&runCommand($command);
}
}