From 0f1ac7d42823cf0f47d25f4f0a04620357421589 Mon Sep 17 00:00:00 2001
From: Bo Li <bli@cs.wisc.edu>
Date: Mon, 25 Apr 2011 14:00:49 -0500
Subject: [PATCH] add feature that jump lines with # in gtf

---
 extractRef.cpp            | 1 +
 rsem-calculate-expression | 6 ++++--
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/extractRef.cpp b/extractRef.cpp
index c4f24a9..12b3222 100644
--- 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 1535147..06604d9 100755
--- 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
-- 
2.39.2