X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rsem-plot-transcript-wiggles;h=46a71aaee21ea7abc7d45533db12b93812c7230a;hb=a1dc3c6c442d288c7f4218cbb8b7a54f08e9d980;hp=5054f5bc0d4fa3256bc4ac4899162c4b4e570847;hpb=fc69cf6af24c0550e55447fc82f01cb6f90c1c42;p=rsem.git

diff --git a/rsem-plot-transcript-wiggles b/rsem-plot-transcript-wiggles
index 5054f5b..46a71aa 100755
--- a/rsem-plot-transcript-wiggles
+++ b/rsem-plot-transcript-wiggles
@@ -19,8 +19,12 @@ pod2usage(-msg => "Invalid number of arguments!", -exitval => 2, -verbose => 2)
 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);
 }
 
@@ -34,7 +38,7 @@ if ($show_unique) {
 	&runCommand($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);
     }
 }
@@ -42,6 +46,7 @@ if ($show_unique) {
 $command = $dir."rsem-gen-transcript-plots $ARGV[0] $ARGV[1] $gene_list $show_unique $ARGV[2]";
 &runCommand($command);
 
+
 # command, {err_msg}
 sub runCommand {
     print $_[0]."\n";
@@ -49,7 +54,7 @@ sub runCommand {
     if ($status != 0) { 
 	my $errmsg;
 	if (scalar(@_) > 1) { $errmsg = $_[1]; }
-	else { $errmsg = "\"$command\" failed! Plase check if you provide correct parameters/options for the pipeline!"; }
+	else { $errmsg = "\"$command\" failed! Please check if you provide correct parameters/options for the pipeline!"; }
 	print $errmsg."\n";
 	exit(-1);
     }