add feature that jump lines with # in gtf

diff --git a/extractRef.cpp b/extractRef.cpp
index c4f24a9a079b37a25d39d6fa969ff9ac1482f3de..12b3222744db41cf1602890b9ae0fccfd2dfedca 100644 (file)
--- a/extractRef.cpp
+++ b/extractRef.cpp
@@ -113,6 +113,7 @@ void parse_gtf_file(char* gtfF) {
 
        items.clear();
        while (getline(fin, line)) {
+               if (line[0] == '#') continue; // if this line is comment, jump it
                item.parse(line);
                string feature = item.getFeature();
                if (feature == "exon") {

diff --git a/rsem-calculate-expression b/rsem-calculate-expression
index 1535147976a811383f030d41c64768f6e590cefa..06604d96a8c415b4eaeaf9e74854d6bf772a8d17 100755 (executable)
--- a/rsem-calculate-expression
+++ b/rsem-calculate-expression
@@ -8,7 +8,7 @@ use strict;
 
 #const
 my $BURNIN = 200;
-my $NSAMPLES = 1000;
+my $CHAINLEN = 1000;
 my $SAMPLEGAP = 1;
 my $CONFIDENCE = 0.95;
 my $NSPC = 50;
@@ -285,7 +285,7 @@ if ($genBamF) {
 &collectResults("$imdName.gene_res", "$sampleName.genes.results"); # gene level
 
 if ($calcCI) {
-    $command = $dir."rsem-run-gibbs $refName $sampleName $sampleToken $BURNIN $NSAMPLES $SAMPLEGAP";
+    $command = $dir."rsem-run-gibbs $refName $sampleName $sampleToken $BURNIN $CHAINLEN $SAMPLEGAP";
 #    $command .= " -p $nThreads";
     if ($quiet) { $command .= " -q"; }
     print "$command\n";
@@ -661,3 +661,5 @@ Assume the path to the bowtie executables is in the user's PATH environment vari
                            mmliver_paired_end_quals
 
 =cut
+
+#  LocalWords:  usr