Fixed a bug related to output format. Grant read permession to all files and executio...

[rsem.git] / rsem-calculate-expression

diff --git a/rsem-calculate-expression b/rsem-calculate-expression
index 3539fa498e76e4c902caa87fdb242433207f65ae..0f22282dfc8f0b4ea259d057b7aca3ebdc2528ce 100755 (executable)
--- a/rsem-calculate-expression
+++ b/rsem-calculate-expression
@@ -344,7 +344,7 @@ sub collectResults {
        ++$cnt;
        chomp($line);
        my @local_arr = split(/\t/, $line);
-       if ($cnt == 3) { @comment = @local_arr; }
+       if ($cnt == 4) { @comment = @local_arr; }
        else { push(@results, \@local_arr); }
     }
     
@@ -396,7 +396,7 @@ Comma-separated list of files containing downstream reads which are paired with
 
 =item B<input>
 
-SAM/BAM formatted input file.  If "-" is specified for the filename, SAM/BAM input is instead assumed to come from standard input. SAM/BAM format used is SAM Spec v1.2. RSEM requires all alignments of the same read group together. For paired-end reads, RSEM also requires the two mates of any alignment be adjacent. See Description section for how to make input file obey RSEM's requirements.
+SAM/BAM formatted input file.  If "-" is specified for the filename, SAM/BAM input is instead assumed to come from standard input. RSEM requires all alignments of the same read group together. For paired-end reads, RSEM also requires the two mates of any alignment be adjacent. See Description section for how to make input file obey RSEM's requirements.
 
 =item B<reference_name>                        
 
@@ -538,7 +538,7 @@ One simple way to make the alignment file (e.g. input.sam) satisfying RSEM's req
 
   sort -k 1,1 -s input.sam > input.sorted.sam
 
-The SAM/BAM format RSEM uses is v1.2.
+The SAM/BAM format RSEM uses is v1.3. However, it is compatible with old SAM/BAM format. 
 
 The user must run 'rsem-prepare-reference' with the appropriate reference before using this program.