From: Bo Li <bli@cs.wisc.edu>
Date: Wed, 14 Dec 2011 22:40:52 +0000 (-0600)
Subject: modify one error message and add --bowtie-chunkmbs option by merging earonesty's... 
X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=commitdiff_plain;h=64cbcf77f3d0a6d8dea12d4c2a6500399d9bd2a2

modify one error message and add --bowtie-chunkmbs option by merging earonesty's change
---

diff --git a/extractRef.cpp b/extractRef.cpp
index 3173d65..da0effc 100644
--- a/extractRef.cpp
+++ b/extractRef.cpp
@@ -304,8 +304,7 @@ int main(int argc, char* argv[]) {
 	for (int i = 1; i <= M; i++) {
 		if (seqs[i] == "") {
 			const Transcript& transcript = transcripts.getTranscriptAt(i);
-			fprintf(stderr, "Cannot extract transcript %s's sequence from chromosome %s, whose information might not be provided! \"
-					"Please check if the chromosome directory is set correctly or the list of chromosome files is complete.\n", \
+			fprintf(stderr, "Cannot extract transcript %s's sequence from chromosome %s, whose information might not be provided! Please check if the chromosome directory is set correctly or the list of chromosome files is complete.\n", \
 					transcript.getTranscriptID().c_str(), transcript.getGeneID().c_str());
 			exit(-1);
 		}
diff --git a/rsem-calculate-expression b/rsem-calculate-expression
index bc976c3..d50a6c2 100755
--- a/rsem-calculate-expression
+++ b/rsem-calculate-expression
@@ -191,16 +191,14 @@ if (!$is_sam && !$is_bam) {
     else { print "Oh, no!!!"; exit(2); }
     
     $command .= " -n $C -e $E -l $L";
-    
     if ($read_type == 2 || $read_type == 3) { $command .= " -I $minL -X $maxL"; }
+    if ($chunkMbs > 0) { $command .= " --chunkmbs $chunkMbs"; }
     
     if ($strand_specific || $probF == 1.0) { $command .= " --norc"; }
     elsif ($probF == 0.0) { $command .= " --nofw"; }
 
     $command .= " -p $nThreads -a -m $maxHits -S";
-    if ($quiet) { $command .= " --quiet"; }
-    
-    $command .= " --chunkmbs $chunkMbs" if $chunkMbs > 0;
+    if ($quiet) { $command .= " --quiet"; }    
 
     $command .= " $refName";
     if ($read_type == 0 || $read_type == 1) {