Fix various bugs

tags/drap-v1.9/bin/bwa.pl

@@ -231,8 +231,8 @@ MAIN:
 		push( @unmerged_bams, $bam."_".$file_idx ); 
 		my $cmd = new CmdSet( undef, undef, "bwa.pl-3", $scheduler );
 		$cmd->add_cmd( new Cmd("samtools view -bS -@ ".$cpu." ".$sam." > ".$unsorted_bam, $cpu, $mem, $vmem) );
-		$cmd->add_cmd( new Cmd("samtools sort -@ ".$cpu." ".$unsorted_bam." ".$bam, $cpu, $mem, $vmem) );
-		$cmd->add_cmd( new Cmd("mv ".$bam.".bam ".$unmerged_bams[$file_idx], $cpu, $mem, $vmem) );
+		$cmd->add_cmd( new Cmd("samtools sort -@ ".$cpu." -O bam -o ".$bam." ".$unsorted_bam, $cpu, $mem, $vmem) );
+		$cmd->add_cmd( new Cmd("mv ".$bam." ".$unmerged_bams[$file_idx], $cpu, $mem, $vmem) );
 		$cmd->submit();
 		unlink( $unsorted_bam );
 		unlink( $sam );

tags/drap-v1.91/doc/install.html

@@ -342,7 +342,7 @@ type = local  # This value can be 'local' or 'sge'
 				<p>If one of the software listed in the section SOFTWARES is not directly accessible, add the bin folder of this software in the section PATH (see '<a href="#check_dependencies">Check dependencies installation</a>').</p>
 <pre>
 [ENV] # Commands to execute to set the environnement (i.e. module load)
-preprocess_env = module load compiler/gcc-4.9.1 # for Khmer package
+preprocess_env = module load compiler/gcc-4.9.1; ... # for Khmer package
 ...
 </pre>
 				<p>If one of the software listed in the section SOFTWARES need a specific environment, add the commands to execute to complete the step using this specific tool in this section. The example above shows how to load a module named compiler/gcc-4.9.1 needed to run scripts from the Khmer package. Scripts from this package are used to complete the preprocess step (see the <a href="third_party_tools.html">DRAP 3rd Party Tools</a> table), so you should give the step name followed by _env and the command to execute at the step start.