Merge remote-tracking branch 'origin/master'

diff --git a/rsem-calculate-expression b/rsem-calculate-expression
index f90ec4814891280e7c7b12691b5bdcb7ebfa3fbe..bc976c32269a2938cb0607dabc36157e58509ffb 100755 (executable)
--- a/rsem-calculate-expression
+++ b/rsem-calculate-expression
@@ -24,6 +24,7 @@ my $C = 2;
 my $E = 99999999;
 my $L = 25;
 my $maxHits = 200;
+my $chunkMbs = 0;      # 0 = use bowtie default
 my $phred33 = 0;
 my $phred64 = 0;
 my $solexa = 0;
@@ -73,6 +74,7 @@ GetOptions("keep-intermediate-files" => \$keep_intermediate_files,
           "bowtie-n=i" => \$C,
           "bowtie-e=i" => \$E,
           "bowtie-m=i" => \$maxHits,
+          "bowtie-chunkmbs=i" => \$chunkMbs,
           "phred33-quals" => \$phred33,
           "phred64-quals" => \$phred64, #solexa1.3-quals" => \$phred64,
           "solexa-quals" => \$solexa,
@@ -198,6 +200,8 @@ if (!$is_sam && !$is_bam) {
     $command .= " -p $nThreads -a -m $maxHits -S";
     if ($quiet) { $command .= " --quiet"; }
     
+    $command .= " --chunkmbs $chunkMbs" if $chunkMbs > 0;
+
     $command .= " $refName";
     if ($read_type == 0 || $read_type == 1) {
        $command .= " $mate1_list"; 
@@ -496,6 +500,10 @@ The path to the bowtie executables. (Default: the path to the bowtie executables
 
 (Bowtie parameter) suppress all alignments for a read if > <int> valid alignments exist. (Default: 200)
 
+=item B<--bowtie-chunkmbs> <int>
+
+(Bowtie parameter) memory allocated for best first alignment calculation (Default: 0 - use bowtie's default)
+
 =item B<--phred33-quals>
 
 Input quality scores are encoded as Phred+33. (Default: on)