v1.1.5.b

[rsem.git] / rsem-calculate-expression

diff --git a/rsem-calculate-expression b/rsem-calculate-expression
index ddeb8ddd4af556a3fea3dc9c194c02722f52ed94..7826ec72680bc551f7c4a167d53e2d9d0b830905 100755 (executable)
--- a/rsem-calculate-expression
+++ b/rsem-calculate-expression
@@ -173,7 +173,7 @@ if (!$is_sam && !$is_bam) {
     if ($read_type == 2 || $read_type == 3) { $command .= " -I $minL -X $maxL"; }
     
     if ($strand_specific || $probF == 1.0) { $command .= " --norc"; }
-    elsif ($probF = 0.0) { $command .= " --nofw"; }
+    elsif ($probF == 0.0) { $command .= " --nofw"; }
 
     $command .= " -p $nThreads -a -m $maxHits -S";
     if ($quiet) { $command .= " --quiet"; }
@@ -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.