Got rid of LibraryComplexity class; moved statistics into things that happen with early exit

    # to be properly created

    if [ -z "$genomePath" ]

    then

        echo "***! You must define a chrom.sizes file via the \"-p\" flag that delineates the lengths of the chromosomes in the genome at $refSeq";

        echo "***! You must define a chrom.sizes file via the \"-p\" flag that delineates the lengths of the chromosomes in the genome at $refSeq; you may use \"-p hg19\" or other standard genomes";

        exit 1;

    fi

fi

fi

## Check that site file exists, needed for fragment number for merged_nodups

if [ ! -e "$site_file" ] && [ "$nofrag" -ne 1 ]

if [ ! -e "$site_file" ] && [ "$site" != "none" ]

then

    echo "***! $site_file does not exist. It must be created before running this script."

    exit 1

    # for consistency with cluster naming in split_rmdups

    mv ${outputdir}/optdups.txt ${outputdir}/opt_dups.txt 

fi

if [ -z "$genomePath" ]

then

    #If no path to genome is give, use genome ID as default.

    genomePath=$genomeID

fi

#CREATE HIC FILES

# if early exit, we stop here, once the merged_nodups.txt file is created.

if [ -z "$earlyexit" ]

then

#STATISTICS

#Skip if post-processing only is required

if [ -z $postproc ]

then        

    export _JAVA_OPTIONS=-Xmx16384m

    export LC_ALL=en_US.UTF-8 

    tail -n1 $headfile | awk '{printf"%-1000s\n", $0}' > $outputdir/inter.txt;

        ${juiceDir}/scripts/common/statistics.pl -s $site_file -l $ligation -o $outputdir/stats_dups.txt $outputdir/dups.txt

    cat $splitdir/*.res.txt | awk -f ${juiceDir}/scripts/common/stats_sub.awk >> $outputdir/inter.txt

        java -cp ${juiceDir}/scripts/common/ LibraryComplexity $outputdir inter.txt >> $outputdir/inter.txt

    ${juiceDir}/scripts/common/juicer_tools LibraryComplexity $outputdir inter.txt >> $outputdir/inter.txt

    cp $outputdir/inter.txt $outputdir/inter_30.txt 

    ${juiceDir}/scripts/common/statistics.pl -s $site_file -l $ligation -o $outputdir/inter.txt -q 1 $outputdir/merged_nodups.txt 

    cat $splitdir/*_abnorm.sam > $outputdir/abnormal.sam

    cat $splitdir/*_unmapped.sam > $outputdir/unmapped.sam

    awk -f ${juiceDir}/scripts/common/collisions.awk $outputdir/abnormal.sam > $outputdir/collisions.txt

    # Collisions dedupping script goes here

fi

if [ -z "$genomePath" ]

then

    #If no path to genome is give, use genome ID as default.

    genomePath=$genomeID

fi

#CREATE HIC FILES

# if early exit, we stop here, once the statistics are calculated

if [ -z "$earlyexit" ]

then

    #Skip if post-processing only is required

    if [ -z $postproc ]

    then        

        if [ "$nofrag" -eq 1 ]

        then 

            ${juiceDir}/scripts/common/juicer_tools pre -s $outputdir/inter.txt -g $outputdir/inter_hists.m -q 1 $outputdir/merged_nodups.txt $outputdir/inter.hic $genomePath

        else 

            ${juiceDir}/scripts/common/juicer_tools pre -f $site_file -s $outputdir/inter.txt -g $outputdir/inter_hists.m -q 1 $outputdir/merged_nodups.txt $outputdir/inter.hic $genomePath 

        fi 

	tail -n1 $headfile | awk '{printf"%-1000s\n", $0}' > $outputdir/inter_30.txt;

        cat $splitdir/*.res.txt | awk -f ${juiceDir}/scripts/common/stats_sub.awk >> $outputdir/inter_30.txt

        java -cp ${juiceDir}/scripts/common/ LibraryComplexity $outputdir inter_30.txt >> $outputdir/inter_30.txt

        ${juiceDir}/scripts/common/statistics.pl -s $site_file -l $ligation -o $outputdir/inter_30.txt -q 30 $outputdir/merged_nodups.txt

        if [ "$nofrag" -eq 1 ]

        then