#
# Read one or more sib-pair pedigree files and corresponding scripts
# combining these into a single pedigree file and script
#
# ped1      ped2      --->    ped3
# phe1      phe1              phe1
# phe2                        phe2
#           phe3              phe3
# mar1                        mar1
# mar2      mar2              mar2
# mar3                        mar3
#           mar4              mar4
#
# Model:
# No individuals are present in more than one pedigree file:
# the output pedigree IDs from each pedigree file are prefixed by the
# position of the file in the argument list eg 1_ped1
#
# Loci may present in more than one pedigree files, 
# and loci of the same name in different scripts are assumed to be
# the same locus.  Phenotypes from different files are put together,
# but since the program cannot know whether markers
# in different files are from the same chromosome, these follow the
# phenotypes in "catped.in" ordered according to their appearance in the 
# original scripts.  A new variable "dataset" identifies which pedigree
# file that family came from.
#
AWK=/usr/bin/gawk
SCRIPT="catped.in"
PEDFILE="catped.ped"

HELP=0
if [ $# = 0 ] || [ $# = 1 ] 
then
  HELP=1
else
  for i in $*
  do
    if [ ! -f $i ]
    then
      HELP=1
      echo "ERROR: $i does not exist"
      echo
    fi
  done 
fi

if [ $HELP = 1 ]
then
	echo "Usage: catped <script1> <ped_file1> <script2> <ped_file2>..."
        echo "Merge sib-pair type pedigree files and scripts"
        echo "assuming no individual is in more than one pedigree file."
        echo "Loci may present in more than one pedigree files,"
        echo "and loci of the same name in different scripts are assumed identical."
        echo "A new variable \"dataset\" identifies which pedigree"
        echo "file each family came from."
        exit
fi

$AWK  -v file_list="$*" -v script=$SCRIPT -v pedfile=$PEDFILE '
BEGIN { n_files=split(file_list,files)
        if ((n_files % 2)==1) {
          print "ERROR: Must be as many Sib-pair scripts as there are pedigree files"
          exit
        }
        aff["1"]="n"; aff["n"]="n"
        aff["2"]="y"; aff["y"]="y"
        aff["0"]="x"; aff["x"]="x"
#
# Merge the scripts
#
        n_files=n_files/2
        for(i=1;i<=n_files;i++) {
           sp_script=files[2*i-1]
           nloc[i]=0
           pos=5
           while (getline < sp_script) {
             if ($1=="set" && substr($2,1,3)=="loc") {
               name=$3
               type=substr($4,1,3)
               mpos=$5
               
               master[name]=master[name] " " i
               nloc[i]++
               loc[i,nloc[i]]=name
               loctyp[i,name]=type
               mappos[i,name]=mpos
               locpos[i,name]=pos+1
               if (type=="mar") {
                 pos+=2
               }else{
                 pos++ 
               }
             }
           }
           close(sp_script)
        }
#
# Phenotypes
#
        print "set locus dataset    qua" > script

        nfinal=0
        for(i=1;i<=n_files;i++) {
          for (j=1;j<=nloc[i];j++) {
            name=loc[i,j]
            type=loctyp[i,name]
            nsets=split(master[name],sets)
            if ( type != "mar" && i==sets[1]) {
              nfinal++
              final[nfinal]=name
              fintyp[nfinal]=type 
              printf "set locus %-10s %3s\n", \
                     name, loctyp[sets[1],name] >  script
            }
          }
        }
#
# Genotypes
#
        for (i=1;i<=n_files;i++) {
          for (j=1;j<=nloc[i];j++) {
            name=loc[i,j]
            type=loctyp[i,name]
            nsets=split(master[name],sets)
            if ( type == "mar" && i==sets[1]) {
              nfinal++
              final[nfinal]=name
              fintyp[nfinal]=type 
              printf "set locus %-10s %3s %8.2f\n",\
                     name, loctyp[i,name], mappos[i,name] > script
            }
          }
        }
        print "read pedigree " pedfile "\nrun\n" > script
#
# Merge the pedigrees
#
        for(i=1;i<=n_files;i++) {
           sp_ped=files[2*i]
           while (getline < sp_ped) { 
             if (substr($1,1,1)=="!") {
               print $0
             }else{
               fa=$3
               mo=$4
               sex=$5
               if (fa=="0") fa="x"
               if (mo=="0") mo="x"
               if (sex=="1") {
                 sex="m"
               }else if (sex=="2") {
                 sex="f"
               }
               printf i "_" $1 " " $2 " " fa " " mo " " sex " " i
               for(j=1;j<=nfinal;j++) {
                 type=fintyp[j]
                 if (type=="mar") {
                   if ((i,final[j]) in locpos) {
                     pos=locpos[i,final[j]]
                     printf " %3d %3d", $pos, $(pos+1)
                   }else{
                     printf "   x   x"
                   }
                 }else{
                   if ((i,final[j]) in locpos) {
                     pos=locpos[i,final[j]]
                     val=$pos
                     if (type=="aff") val=aff[val]
                     printf " %s", val 
                   }else{
                     printf " x"
                   }
                 }
               }
               printf "\n"
             }
           }
        }
}' > tmp$$
best tmp$$ > $PEDFILE
rm tmp$$