Fixed bug where multiple fastqs would not be processed. Got rid of unnecessary print out

## Not in merge, dedup, final, or postproc stage, i.e. need to align files.

if [ -z $merge ] && [ -z $final ] && [ -z $dedup ] && [ -z $postproc ]

then

    echo -e "(-: Aligning files matching $fastqdir\n in queue $queue to genome $genomeID with site file $site_file"

    echo -e "(-: Aligning files matching $fastqdir\n to genome $genomeID with site file $site_file"

    if [ ! $splitdirexists ]

    then

        echo "(-: Created $splitdir and $outputdir."

		echo "(-: Mem align of $name2$ext.sam done successfully"

            fi

	fi

    done

        # sort read 1 aligned file by readname

	sort -T $tmpdir -k1,1 $name1$ext.sam > $name1${ext}_sort.sam

	if [ $? -ne 0 ]

	else

            rm $name${ext}_norm.txt $name${ext}.frag.txt

	fi

    done

fi

#MERGE SORTED AND ALIGNED FILES