--- a/runMapping_wrapper.pl	Thu Jul 14 22:14:07 2011 -0400
+++ b/runMapping_wrapper.pl	Wed Dec 21 19:42:53 2011 -0800
@@ -23,6 +23,7 @@
 my $trimmed_reads_fasta=shift @ARGV;
 my $trimmed_reads_qual=shift @ARGV;
 my $contigs_ace=shift @ARGV;
+my $contigs_bam=shift @ARGV;
 my $large_contigs_fasta=shift @ARGV;
 my $large_contigs_qual=shift @ARGV;
 my $gene_status=shift @ARGV;
@@ -32,9 +33,8 @@
 my @cmd=removeUnusedOptions(@ARGV);
 
 # RUN COMMAND
-# NOTE: FIRST ARG EXPECTED TO BE EXECUTABLE
 my $stderr;
-eval { $stderr=`@cmd 2>&1`; };
+eval { $stderr=`runMapping @cmd 2>&1`; };
 if ( $@ ) {
     print STDERR "Newbler ERROR: $stderr\n";
     `cat $outdir/assembly/454NewblerProgress.txt 1>&2`;
@@ -58,6 +58,7 @@
 get_outfile("$outdir/454TrimmedReads.fna", $trimmed_reads_fasta);
 get_outfile("$outdir/454TrimmedReads.qual", $trimmed_reads_qual);
 get_outfile("$outdir/454Contigs.ace", $contigs_ace);
+get_outfile("$outdir/454Contigs.bam", $contigs_bam);
 get_outfile("$outdir/454LargeContigs.fna", $large_contigs_fasta);
 get_outfile("$outdir/454LargeContigs.qual", $large_contigs_qual);
 get_outfile("$outdir/454GeneStatus.txt", $gene_status);