fixing unnecessary check in the check script

# Sanity check once pipeline is complete to be sure number of lines adds up, deduping

# proceeded appropriately, and that files were created

# Juicer version 1.5

if [ -z $ARG1 ]

then

# 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}}'`

then

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

    echo "Stats don't add up.  Check ${outputdir} for results"

        exit 100

    fi

    exit 1

fi

# Check the sizes of merged_sort versus the dups/no dups files to be sure

then

    echo "***! Error! The sorted file and dups/no dups files do not add up, or were empty. Merge or dedupping likely failed, restart pipeline with -S merge or -S dedup"

    echo "Dups don't add up.  Check ${outputdir} for results"

    exit 100

    exit 1

fi

wctotal=`cat ${splitdir}/*_linecount.txt | awk '{sum+=$1}END{print sum/4}'`

check2=`cat ${splitdir}/*norm*res* | awk '{s2+=$2;}END{print s2}'`

if [ -z $ARG1 ] 

then

if [ $wctotal -ne $check2 ]

then

    echo "***! Error! The number of reads in the fastqs (${wctotal}) is not the same as the number of reads reported in the stats (${check2}), likely due to a failure during alignment"

    echo "Reads don't add up.  Check ${outputdir} for results"

        exit 100

    fi

    exit 1

fi

if [ -f ${outputdir}/inter.hic ] && [ -s ${outputdir}/inter.hic ] && [ -f ${outputdir}/inter_30.hic ] && [ -s ${outputdir}/inter_30.hic ]

else

    echo "***! Error! Either inter.hic or inter_30.hic were not created"

    echo "Either inter.hic or inter_30.hic were not created.  Check ${outputdir} for results"

    exit 100

    exit 1

fi

# Sanity check once pipeline is complete to be sure number of lines adds up, deduping

# proceeded appropriately, and that files were created

# Juicer version 1.5

if [ -z $ARG1 ]

then

# 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}}'`

then

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

    echo "Stats don't add up.  Check ${outputdir} for results"

        exit 100

    fi

    exit 1

fi

# Check the sizes of merged_sort versus the dups/no dups files to be sure

then

    echo "***! Error! The sorted file and dups/no dups files do not add up, or were empty. Merge or dedupping likely failed, restart pipeline with -S merge or -S dedup"

    echo "Dups don't add up.  Check ${outputdir} for results"

    exit 100

    exit 1

fi

wctotal=`cat ${splitdir}/*_linecount.txt | awk '{sum+=$1}END{print sum/4}'`

check2=`cat ${splitdir}/*norm*res* | awk '{s2+=$2;}END{print s2}'`

if [ -z $ARG1 ] 

then

if [ $wctotal -ne $check2 ]

then

    echo "***! Error! The number of reads in the fastqs (${wctotal}) is not the same as the number of reads reported in the stats (${check2}), likely due to a failure during alignment"

    echo "Reads don't add up.  Check ${outputdir} for results"

        exit 100

    fi

    exit 1

fi

if [ -f ${outputdir}/inter.hic ] && [ -s ${outputdir}/inter.hic ] && [ -f ${outputdir}/inter_30.hic ] && [ -s ${outputdir}/inter_30.hic ]

else

    echo "***! Error! Either inter.hic or inter_30.hic were not created"

    echo "Either inter.hic or inter_30.hic were not created.  Check ${outputdir} for results"

    exit 100

    exit 1

fi

# Sanity check once pipeline is complete to be sure number of lines adds up, deduping

# proceeded appropriately, and that files were created

# Juicer version 1.5

if [ -z $ARG1 ]

then

# 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}}'`

then

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

    echo "Stats don't add up.  Check ${outputdir} for results"

        exit 100

    fi

    exit 1

fi

# Check the sizes of merged_sort versus the dups/no dups files to be sure

then

    echo "***! Error! The sorted file and dups/no dups files do not add up, or were empty. Merge or dedupping likely failed, restart pipeline with -S merge or -S dedup"

    echo "Dups don't add up.  Check ${outputdir} for results"

    exit 100

    exit 1

fi

wctotal=`cat ${splitdir}/*_linecount.txt | awk '{sum+=$1}END{print sum/4}'`

check2=`cat ${splitdir}/*norm*res* | awk '{s2+=$2;}END{print s2}'`

if [ -z $ARG1 ] 

then

if [ $wctotal -ne $check2 ]

then

    echo "***! Error! The number of reads in the fastqs (${wctotal}) is not the same as the number of reads reported in the stats (${check2}), likely due to a failure during alignment"

    echo "Reads don't add up.  Check ${outputdir} for results"

        exit 100

    fi

    exit 1

fi

if [ -f ${outputdir}/inter.hic ] && [ -s ${outputdir}/inter.hic ] && [ -f ${outputdir}/inter_30.hic ] && [ -s ${outputdir}/inter_30.hic ]

else

    echo "***! Error! Either inter.hic or inter_30.hic were not created"

    echo "Either inter.hic or inter_30.hic were not created.  Check ${outputdir} for results"

    exit 100

    exit 1

fi

# Sanity check once pipeline is complete to be sure number of lines adds up, deduping

# proceeded appropriately, and that files were created

# Juicer version 1.5

if [ -z $ARG1 ]

then

# 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}}'`

then

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

    echo "Stats don't add up.  Check ${outputdir} for results"

        exit 100

    fi

    exit 1

fi

# Check the sizes of merged_sort versus the dups/no dups files to be sure

then

    echo "***! Error! The sorted file and dups/no dups files do not add up, or were empty. Merge or dedupping likely failed, restart pipeline with -S merge or -S dedup"

    echo "Dups don't add up.  Check ${outputdir} for results"

    exit 100

    exit 1

fi

wctotal=`cat ${splitdir}/*_linecount.txt | awk '{sum+=$1}END{print sum/4}'`

check2=`cat ${splitdir}/*norm*res* | awk '{s2+=$2;}END{print s2}'`

if [ -z $ARG1 ] 

then

if [ $wctotal -ne $check2 ]

then

    echo "***! Error! The number of reads in the fastqs (${wctotal}) is not the same as the number of reads reported in the stats (${check2}), likely due to a failure during alignment"

    echo "Reads don't add up.  Check ${outputdir} for results"

        exit 100

    fi

    exit 1

fi

if [ -f ${outputdir}/inter.hic ] && [ -s ${outputdir}/inter.hic ] && [ -f ${outputdir}/inter_30.hic ] && [ -s ${outputdir}/inter_30.hic ]

else

    echo "***! Error! Either inter.hic or inter_30.hic were not created"

    echo "Either inter.hic or inter_30.hic were not created.  Check ${outputdir} for results"

    exit 100

    exit 1

fi

# Sanity check once pipeline is complete to be sure number of lines adds up, deduping

# proceeded appropriately, and that files were created

# Juicer version 1.5

if [ -z $ARG1 ]

then

# 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}}'`

then

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

    echo "Stats don't add up.  Check ${outputdir} for results"

        exit 100

    fi

    exit 1

fi

# Check the sizes of merged_sort versus the dups/no dups files to be sure

then

    echo "***! Error! The sorted file and dups/no dups files do not add up, or were empty. Merge or dedupping likely failed, restart pipeline with -S merge or -S dedup"

    echo "Dups don't add up.  Check ${outputdir} for results"

    exit 100

    exit 1

fi

wctotal=`cat ${splitdir}/*_linecount.txt | awk '{sum+=$1}END{print sum/4}'`

check2=`cat ${splitdir}/*norm*res* | awk '{s2+=$2;}END{print s2}'`

if [ -z $ARG1 ] 

then

if [ $wctotal -ne $check2 ]

then

    echo "***! Error! The number of reads in the fastqs (${wctotal}) is not the same as the number of reads reported in the stats (${check2}), likely due to a failure during alignment"

    echo "Reads don't add up.  Check ${outputdir} for results"

        exit 100

    fi

    exit 1

fi

if [ -f ${outputdir}/inter.hic ] && [ -s ${outputdir}/inter.hic ] && [ -f ${outputdir}/inter_30.hic ] && [ -s ${outputdir}/inter_30.hic ]

else

    echo "***! Error! Either inter.hic or inter_30.hic were not created"

    echo "Either inter.hic or inter_30.hic were not created.  Check ${outputdir} for results"

    exit 100

    exit 1

fi