diff --git a/extras/run-bwamem b/extras/run-bwamem
index 3231a6e..40724bb 100755
--- a/extras/run-bwamem
+++ b/extras/run-bwamem
@@ -5,7 +5,7 @@ use warnings;
 use Getopt::Std;
 
 my %opts = (t=>1, n=>64);
-getopts("SpAdsko:R:x:t:", \%opts);
+getopts("Spadsko:R:x:t:", \%opts);
 
 die('
 Usage:   run-bwamem [options] <idxbase> <file1> [file2]
@@ -19,10 +19,10 @@ Options: -o STR    prefix for output files                       [inferred from
          -t INT    number of threads                                               [1]
          -p        input are paired-end reads if file2 absent
 
-         -A        skip HiSeq2000/2500 PE resequencing adapter trimming (via trimadap)
+         -a        trim HiSeq2000/2500 PE resequencing adapters (via trimadap)
          -d        mark duplicate (via samblaster)
          -S        for SAM/BAM input, don\'t shuffle
-         -s        sort the output alignment (more RAM)
+         -s        sort the output alignment (higher RAM footprint)
          -k        keep temporary files generated by typeHLA
 
 Note: File type is determined by the file extension of the first input sequence file.
@@ -95,8 +95,7 @@ my $is_sam = $ARGV[1] =~ /\.(sam|sam\.gz)$/? 1 : 0;
 my $is_bam = $ARGV[1] =~ /\.bam$/? 1 : 0;
 
 if (defined($opts{x})) {
-	$opts{A} = 1; delete($opts{d});
-	delete $opts{p};
+	delete($opts{d}); delete($opts{a}); delete $opts{p};
 }
 
 my $cmd = '';
@@ -115,7 +114,7 @@ if ($is_sam || $is_bam) {
 
 my $bwa_opts = ($opts{t} > 1? "-t$opts{t} " : "") . (defined($opts{x})? "-x $opts{x} " : "") . (defined($opts{R})? "-R'$opts{R}' " : "");
 
-$cmd .= "  | $root/trimadap \\\n" unless defined($opts{A});
+$cmd .= "  | $root/trimadap \\\n" if defined($opts{a});
 $cmd .= "  | $root/bwa mem $bwa_opts" . ($is_pe? "-p " : "") . "$ARGV[0] - 2> $prefix.log.bwamem \\\n";
 $cmd .= "  | $root/samblaster 2> $prefix.log.dedup \\\n" if defined($opts{d});
 
@@ -136,8 +135,10 @@ $cmd .= defined($opts{s})? "  | $root/samtools sort -@ $t_sort -m1G - $prefix.al
 
 # map single end reads
 if ($cmd =~ /$prefix.oph.fq.gz/) {
-	$cmd .= "[ -s $prefix.oph.fq.gz ] && ";
-	$cmd .= "$root/bwa mem $bwa_opts$ARGV[0] $prefix.oph.fq.gz 2>> $prefix.log.bwamem | gzip -1 > $prefix.oph.sam.gz; rm -f $prefix.oph.fq.gz;\n";
+	$cmd .= "[ -s $prefix.oph.fq.gz ] && zcat $prefix.oph.fq.gz \\\n";
+	$cmd .= "  | $root/trimadap \\\n" if defined($opts{a});
+	$cmd .= "  | $root/bwa mem $bwa_opts$ARGV[0] - 2>> $prefix.log.bwamem | gzip -1 > $prefix.oph.sam.gz;\n";
+	$cmd .= "rm -f $prefix.oph.fq.gz;\n";
 }
 
 if ($has_hla && (!defined($opts{x}) || $opts{x} eq 'intractg')) {