X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rsem-calculate-expression;h=7826ec72680bc551f7c4a167d53e2d9d0b830905;hb=a2a1417f57577d69c7d17c5fba40c2aa90510406;hp=dfb5052cca2b163c605c20cf08426e0e0092f062;hpb=a95154919f950f86de9104b2b9dcf1f0c7e83387;p=rsem.git

diff --git a/rsem-calculate-expression b/rsem-calculate-expression
index dfb5052..7826ec7 100755
--- a/rsem-calculate-expression
+++ b/rsem-calculate-expression
@@ -93,7 +93,7 @@ pod2usage(-verbose => 2) if ($help == 1);
 if ($is_sam || $is_bam) {
     pod2usage(-msg => "Invalid number of arguments!", -exitval => 2, -verbose => 2) if (scalar(@ARGV) != 3);
     pod2usage(-msg => "--sam and --bam cannot be active at the same time!", -exitval => 2, -verbose => 2) if ($is_sam == 1&& $is_bam == 1);
-    pod2usage(-msg => "--bowtie-path, --bowtie-n, --bowtie-e, --bowtie-m, --phred33-quals, --phred64-quals or --solexa-quals cannot be set if input is SAM/BAM format!", -exitval => 2, -verbose => 2) if ($bowtie_path ne "" || $C != 2 || $E != 999999 || $maxHits != 200 || $phred33 || $phred64 || $solexa);
+    pod2usage(-msg => "--bowtie-path, --bowtie-n, --bowtie-e, --bowtie-m, --phred33-quals, --phred64-quals or --solexa-quals cannot be set if input is SAM/BAM format!", -exitval => 2, -verbose => 2) if ($bowtie_path ne "" || $C != 2 || $E != 99999999 || $maxHits != 200 || $phred33 || $phred64 || $solexa);
 }
 else {
     pod2usage(-msg => "Invalid number of arguments!", -exitval => 2, -verbose => 2) if (!$paired_end && scalar(@ARGV) != 3 || $paired_end && scalar(@ARGV) != 4);    
@@ -173,7 +173,7 @@ if (!$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.