X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rsem-prepare-reference;h=5d954a1fc7b7f411fa8fe46d43b5cda1cb181fa6;hb=52f1bd6f44f9b2630b839f192fb9ece18581983b;hp=80a954942031c88f6e6e50eb3fd84c86793ad20a;hpb=4a5e5138d3fc409e7ade5c14de7689612290f74f;p=rsem.git

diff --git a/rsem-prepare-reference b/rsem-prepare-reference
index 80a9549..5d954a1 100755
--- a/rsem-prepare-reference
+++ b/rsem-prepare-reference
@@ -5,6 +5,8 @@ use Pod::Usage;
 use File::Basename;
 use strict;
 
+use rsem_perl_utils;
+
 my $status;
 
 my $gtfF = "";
@@ -93,20 +95,6 @@ if (!$no_bowtie) {
     &runCommand($command);
 }
 
-# command, {err_msg}
-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);
-    }
-    print "\n";
-}
-
 __END__
 
 =head1 NAME
@@ -164,7 +152,7 @@ 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 +195,7 @@ 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