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

diff --git a/extractRef.cpp b/extractRef.cpp
index 3173d6517c1fccd6edcf03fa15502b64faadb28d..da0effc70e3c3fe25925c615d30e40f2c15b55eb 100644 (file)
--- 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 bc976c32269a2938cb0607dabc36157e58509ffb..d50a6c2ed9d3997da7a9b54c9a4f54ff5c0512d3 100755 (executable)
--- 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) {