Tidy code

        # remove header, add read end indicator to read name

        awk -f ${juiceDir}/scripts/read1_sortproc.awk \${name1}\${ext}_sort.sam > \${name1}\${ext}_sort1.sam

        awk -f ${juiceDir}/scripts/read2_sortproc.awk \${name2}\${ext}_sort.sam > \${name2}\${ext}_sort1.sam    

        echo "below is the number of lines in \${name1}\${ext}_sort1.sam"

        cat \${name1}\${ext}_sort1.sam | wc -l

        echo "below is the number of lines in \${name2}\${ext}_sort1.sam"

            exit 1

        else

            rm \${name1}\${ext}.sa* \${name2}\${ext}.sa* \${name1}\${ext}_sort*.sam \${name2}\${ext}_sort*.sam

            echo "\${name}\$next.sam created successfully."

            echo "\${name}\$\{ext}.sam created successfully."

        fi

        echo "below is the number of lines in \${name}\${ext}_sort.sam after merging sorted aln1 and aln2"

        cat \${name}\${ext}_sort.sam | wc -l

        echo "below is the number of lines in \${name}\${ext}.sam after merging sorted aln1 and aln2"

        cat \${name}\${ext}.sam | wc -l

MRGALL

    wait

    #done fastq alignment && alignment jobs failure checking.

fi

wait    

jID_alignwrap=$( qstat | grep AlnWrp${groupname} | cut -d ' ' -f 1 )

if [ -z $merge ]

then