mostly working version of 1.6

# Start by checking the statistics to see if they add up 

res1=`cat ${splitdir}/*norm*res*`

check1=`cat ${splitdir}/*norm*res* | awk '{s2+=$2; s3+=$3; s4+=$4; s5+=$5; s6+=$6}END{if (s2 != s3+s4+s5+s6){print 0}else{print 1}}'`

check1=`cat ${splitdir}/*norm*res* | awk '{s2+=$2; s3+=$3; s4+=$4; s5+=$5; s6+=$6; s7+=$7}END{if (s2 != s3+s4+s5+s6+s7){print 0}else{print 1}}'`

if [ $check1 -eq 0 ] || [ -z "$res1" ]

then

    echo "***! Error! The statistics do not add up. Alignment likely failed to complete on one or more files. Run relaunch_prep.sh"

a4+=$5; # chimeric ambiguous

a5+=$6; # unmapped

a6+=$1; # ligations 

a7+=$7; # mapq0

}

END{

    printf("Sequenced Read Pairs:  %'d\n Normal Paired: %'d (%0.2f%)\n Chimeric Paired: %'d (%0.2f%)\n Chimeric Ambiguous: %'d (%0.2f%)\n Unmapped: %'d (%0.2f%)\n Ligation Motif Present: %'d (%0.2f%)\nAlignable (Normal+Chimeric Paired): %'d (%0.2f%)\n", a1, a3, a3*100/a1, a4, a4*100/a1, a5, a5*100/a1, a2, a2*100/a1, a6, a6*100/a1, a3+a4, (a3+a4)*100/a1);

    printf("Sequenced Read Pairs:  %'d\n Normal Paired: %'d (%0.2f%)\n Chimeric Paired: %'d (%0.2f%)\n Chimeric Ambiguous: %'d (%0.2f%)\n Unmapped: %'d (%0.2f%)\n MAPQ 0: %'d (%0.2f%)\n Ligation Motif Present: %'d (%0.2f%)\nAlignable (Normal+Chimeric Paired): %'d (%0.2f%)\n", a1, a3, a3*100/a1, a4, a4*100/a1, a5, a5*100/a1, a2, a2*100/a1, a7, a7*100/a1, a6, a6*100/a1, a3+a4, (a3+a4)*100/a1);

}