Updated EBSeq to v1.1.5

[rsem.git] / rsem-prepare-reference

diff --git a/rsem-prepare-reference b/rsem-prepare-reference
index 80a954942031c88f6e6e50eb3fd84c86793ad20a..6c5d5f31ad1dcfc98bec5f999b1bcc7d6eb3eaae 100755 (executable)
--- a/rsem-prepare-reference
+++ b/rsem-prepare-reference
@@ -97,12 +97,12 @@ if (!$no_bowtie) {
 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 $errmsg."\n";
-       exit(-1);
+    if ($status != 0) {
+        my $errmsg = "";
+        if (scalar(@_) > 1) { $errmsg .= $_[1]."\n"; }
+        $errmsg .= "\"$_[0]\" failed! Please check if you provide correct parameters/options for the pipeline!\n";
+        print $errmsg;
+        exit(-1);
     }
     print "\n";
 }
@@ -164,7 +164,7 @@ If this option is off, then the mapping of isoforms to genes depends on whether
 
 =item B<--no-polyA>
 
-Do not add poly(A) tails to the end of reference isoforms. (Default: add poly(A) tails to all transcripts)
+Do not add poly(A) tails to the end of reference isoforms. (Default: adding poly(A) tails to all transcripts)
 
 =item B<--no-polyA-subset> <file>
 
@@ -207,7 +207,7 @@ This program will generate 'reference_name.grp', 'reference_name.ti', 'reference
 
 'reference_name.grp', 'reference_name.ti', 'reference_name.seq', 'reference_name.idx.fa', and 'reference_name.chrlist' are used by RSEM internally.
 
-B<'reference_name.transcripts.fa'> contains the extracted reference transcripts in FASTA format. Poly(A) tails are not added.
+B<'reference_name.transcripts.fa'> contains the extracted reference transcripts in FASTA format. Poly(A) tails are added unless '--no-polyA' is set.
 
 =head1 EXAMPLES