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;
"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,
$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";
(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)