added ligation and threads flag to CPU version

nofrag=0

## Read arguments                                                     

usageHelp="Usage: ${0##*/} [-g genomeID] [-d topDir] [-s site] [-a about] [-R end]\n                 [-S stage] [-p chrom.sizes path] [-y restriction site file]\n                 [-z reference genome file] [-D Juicer scripts directory]\n                 [-r] [-h] [-x]"

usageHelp="Usage: ${0##*/} [-g genomeID] [-d topDir] [-s site] [-a about] [-R end]\n                 [-S stage] [-p chrom.sizes path] [-y restriction site file]\n                 [-z reference genome file] [-D Juicer scripts directory]\n                 [-b ligation] [-t threads] [-r] [-h] [-x]"

genomeHelp="* [genomeID] must be defined in the script, e.g. \"hg19\" or \"mm10\" (default \n  \"$genomeID\"); alternatively, it can be defined using the -z command"

dirHelp="* [topDir] is the top level directory (default\n  \"$topDir\")\n     [topDir]/fastq must contain the fastq files\n     [topDir]/splits will be created to contain the temporary split files\n     [topDir]/aligned will be created for the final alignment"

siteHelp="* [site] must be defined in the script, e.g.  \"HindIII\" or \"MboI\" \n  (default \"$site\")"

siteFileHelp="* [restriction site file]: enter path for restriction site file (locations of\n  restriction sites in genome; can be generated with the script\n  misc/generate_site_positions.py)"

scriptDirHelp="* [Juicer scripts directory]: set the Juicer directory,\n  which should have scripts/ references/ and restriction_sites/ underneath it\n  (default ${juiceDir})"

refSeqHelp="* [reference genome file]: enter path for reference sequence file, BWA index\n  files must be in same directory"

ligationHelp="* [ligation junction]: use this string when counting ligation junctions"

threadsHelp="* [threads]: number of threads when running BWA alignment"

excludeHelp="* -x: exclude fragment-delimited maps from hic file creation"

helpHelp="* -h: print this help and exit"

    echo -e "$siteFileHelp"

    echo -e "$refSeqHelp"

    echo -e "$scriptDirHelp"

    echo -e "$ligationHelp"

    echo -e "$threadsHelp"

    echo "$excludeHelp"

    echo "$helpHelp"

    exit "$1"

	S) stage=$OPTARG ;;

	D) juiceDir=$OPTARG ;;

	x) nofrag=1 ;; #no fragment maps

	b) ligation=$OPTARG ;;

        t) threads=$OPTARG ;;

	[?]) printHelpAndExit 1;;

    esac

done

    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";

        exit 100;

        exit 1;

    fi

fi

## Check that refSeq exists 

if [ ! -e "$refSeq" ]; then

    echo "***! Reference sequence $refSeq does not exist";

    exit 100;

    exit 1;

fi

## Check that index for refSeq exists

if [ ! -e "${refSeq}.bwt" ]; then

    echo "***! Reference sequence $refSeq does not appear to have been indexed. Please run bwa index on this file before running juicer.";

    exit 100;

    exit 1;

fi

## Set ligation junction based on restriction enzyme

if [ -z "$ligation" ]

then

    case $site in

	HindIII) ligation="AAGCTAGCTT";;

	DpnII) ligation="GATCGATC";;

	    echo "$site not listed as recognized enzyme. Using $site_file as site file"

	    echo "Ligation junction is undefined"

    esac

fi

## If DNAse-type experiment, no fragment maps

if [ "$site" == "none" ]

    2) ;;

    *)	echo "$usageHelp"

	echo "$shortHelp2"

	exit 100

	exit 1

esac

if [ -z "$site_file" ]

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

then

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

    exit 100

    exit 1

fi

## Set threads for sending appropriate parameters to cluster and string for BWA call

if [ ! -z "$threads" ]

then

    threadstring="-t $threads"

else

    threads="$(getconf _NPROCESSORS_ONLN)"

    threadstring="-t $threads"

fi

## Directories to be created and regex strings for listing files

    echo "Directory \"$topDir/fastq\" does not exist."

    echo "Create \"$topDir/fastq\" and put fastq files to be aligned there."

    echo "Type \"juicer.sh -h\" for help"

    exit 100

    exit 1

else 

    if stat -t ${fastqdir} >/dev/null 2>&1

    then

	if [ ! -d "$splitdir" ]; then 

	    echo "***! Failed to find any files matching ${fastqdir}"

	    echo "***! Type \"juicer.sh -h \" for help"

	    exit 100		

	    exit 1		

	fi

    fi

fi

then

    echo "***! Move or remove directory \"$outputdir\" before proceeding."

    echo "***! Type \"juicer.sh -h \" for help"

    exit 100			

    exit 1			

else

    if [[ -z "$final" && -z "$dedup" && -z "$merge" && -z "$postproc" ]]; then

        mkdir "$outputdir" || { echo "***! Unable to create ${outputdir}, check permissions." ; exit 100; } 

        mkdir "$outputdir" || { echo "***! Unable to create ${outputdir}, check permissions." ; exit 1; } 

    fi

fi

if [ -d "$splitdir" ]; then

    splitdirexists=1

else

    mkdir "$splitdir" || { echo "***! Unable to create ${splitdir}, check permissions." ; exit 100; }

    mkdir "$splitdir" || { echo "***! Unable to create ${splitdir}, check permissions." ; exit 1; }

fi

## Create temporary directory, used for sort later

## Arguments have been checked and directories created. Now begins

## the real work of the pipeline

threads="-t $(getconf _NPROCESSORS_ONLN)"

testname=$(ls -l ${fastqdir} | awk 'NR==1{print $9}')

if [ "${testname: -3}" == ".gz" ]

then

            if [ $? -ne 0 ]

            then

                echo "***! Alignment of $name1$ext failed."

		            exit 100

		exit 1

            else

                echo "(-: Short align of $name1$ext.sam done successfully"

            fi

        else

            echo "Running command bwa mem $threads $refSeq $name1$ext > $name1$ext.sam" 

            bwa mem $threads $refSeq $name1$ext > $name1$ext.sam

            echo "Running command bwa mem $threadstring $refSeq $name1$ext > $name1$ext.sam" 

            bwa mem $threadstring $refSeq $name1$ext > $name1$ext.sam

            if [ $? -ne 0 ]

            then

                echo "***! Alignment of $name1$ext failed."

                exit 100

                exit 1

            else                                                            

		echo "(-:  Align of $name1$ext.sam done successfully"

            fi                                    

            if [ $? -ne 0 ]

            then

		echo "***! Alignment of $name2$ext failed."

		            exit 100

		exit 1

            else

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

            fi

        else

            echo "Running command bwa mem $threads $refSeq $name2$ext > $name2$ext.sam"

            bwa mem $threads $refSeq $name2$ext > $name2$ext.sam 

            echo "Running command bwa mem $threadstring $refSeq $name2$ext > $name2$ext.sam"

            bwa mem $threadstring $refSeq $name2$ext > $name2$ext.sam 

            if [ $? -ne 0 ]

            then

		echo "***! Alignment of $name2$ext failed."

		            exit 100

		exit 1

            else

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

            fi

    if [ $? -ne 0 ]

    then

        echo "***! Error while sorting $name1$ext.sam"

        exit 100

        exit 1

    else

        echo "(-: Sort read 1 aligned file by readname completed."

    fi

    if [ $? -ne 0 ]

    then

        echo "***! Error while sorting $name2$ext.sam"

        exit 100

        exit 1

    else

        echo "(-: Sort read 2 aligned file by readname completed."

    fi                           

    # add read end indicator to readname

    awk 'BEGIN{OFS="\t"}NF>=11{$1=$1"/1"; print}' $name1${ext}_sort.sam > $name1${ext}_sort1.sam

    awk 'BEGIN{OFS="\t"}NF>=11{$1=$1"/2"; print}' $name2${ext}_sort.sam > $name2${ext}_sort1.sam

#awk 'BEGIN{OFS="\t"}$0 !~ /^@[A-Z][A-Z](\t[A-Za-z][A-Za-z0-9]:[ -~]+)+$/ && $0 !~ /^@CO\t.*/{$1=$1"/1"; print}' $name1${ext}_sort.sam > $name1${ext}_sort1.sam

#awk 'BEGIN{OFS="\t"}$0 !~ /^@[A-Z][A-Z](\t[A-Za-z][A-Za-z0-9]:[ -~]+)+$/ &&$0 !~ /^@CO\t.*/{$1=$1"/2"; print}' $name2${ext}_sort.sam > $name2${ext}_sort1.sam

    # merge the two sorted read end files

    # samtools commands are simply to get header correctly

#    samtools view -bh $name1${ext}_sort.sam > $name1${ext}_sort.bam

#    samtools view -bh $name2${ext}_sort.sam > $name2${ext}_sort.bam

#    samtools merge -n $name$ext.bam $name1${ext}_sort.bam $name2${ext}_sort.bam

#    samtools view -H $name$ext.bam > $name$ext.header.sam  

    sort -T $tmpdir -k1,1 -m $name1${ext}_sort1.sam $name2${ext}_sort1.sam > ${name}${ext}.sam

    if [ $? -ne 0 ]

    then

        echo "***! Failure during merge of read files"

        exit 100

        exit 1

    else

        rm $name1$ext*.sa* $name2$ext*.sa* 

        echo "(-: $name$ext.sam created successfully."

    export LC_ALL=C

    # call chimeric_blacklist.awk to deal with chimeric reads; 

    # sorted file is sorted by read name at this point

    touch $name${ext}_abnorm.sam $name${ext}_unmapped.sam

    awk -v "fname1"=$name${ext}_norm.txt -v "fname2"=$name${ext}_abnorm.sam -v "fname3"=$name${ext}_unmapped.sam -f ${juiceDir}/scripts/common/chimeric_blacklist.awk $name$ext.sam

    if [ $? -ne 0 ]

    then

        echo "***! Failure during chimera handling of $name${ext}"

        exit 100

        exit 1

    fi

    # if any normal reads were written, find what fragment they correspond to 

    # and store that

        awk '{printf("%s %s %s %d %s %s %s %d", $1, $2, $3, 0, $4, $5, $6, 1); for (i=7; i<=NF; i++) {printf(" %s",$i);}printf("\n");}' $name${ext}_norm.txt > $name${ext}.frag.txt

    else                                                                    

        echo "***! No $name${ext}_norm.txt file created"

        exit 100

        exit 1

    fi                                                                      

    if [ $? -ne 0 ]

    then

        echo "***! Failure during fragment assignment of $name${ext}"

        exit 100

        exit 1

    fi                              

     # sort by chromosome, fragment, strand, and position                    

    sort -T $tmpdir -k2,2d -k6,6d -k4,4n -k8,8n -k1,1n -k5,5n -k3,3n $name${ext}.frag.txt > $name${ext}.sort.txt

    if [ $? -ne 0 ]

    then

        echo "***! Failure during sort of $name${ext}"

        exit 100

        exit 1

    else

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

    fi

    if ! sort -T $tmpdir -m -k2,2d -k6,6d -k4,4n -k8,8n -k1,1n -k5,5n -k3,3n $splitdir/*.sort.txt  > $outputdir/merged_sort.txt

    then 

        echo "***! Some problems occurred somewhere in creating sorted align files."

        exit 100

        exit 1

    else

        echo "(-: Finished sorting all sorted files into a single merge."

        rm -r ${tmpdir}