# this script renums pedigrees with metafounders

# so that they are added *before*regular animals

# mf are ascertained because they are not in the 1st column

# also ordered by generation assuming that all metafounders

# start at generation 1

#

#

	function maxval (a,b) { 

		max=b 

		if (a>b){max=a} 

		return max 

	}

BEGIN{

	pos[0]=0 # actual position in the original data file

	changed=1

	posout[0]=0 # position in the new file

	last=0

	cum[0]=0 #number of times it acts as parent

	gen[0]=0

}

# read and store pedigree file

{

	pos[$1]=NR

	dam[$1]=$2

	sire[$1]=$3

	included[$1]=0

	gen[$1]=9999

}

END{

    #printf("%10s%10s\n",NR,"animals") > "/dev/stderr" 

    # find out who is a genetic group

    for (x in sire){

        if(! (sire[x] in pos)){ 

            is_group[sire[x]]=1 

		#printf("%10s%10s\n","sire",sire[x]) > "/dev/stderr"

		cum[sire[x],"sire"]++

	}

    }

    for (x in dam){

        if(! (dam[x] in pos)){ 

            is_group[dam[x]]=1 

		#printf("%10s%10s\n","dam",dam[x]) > "/dev/stderr"

		cum[dam[x],"dam"]++

        }

    }

    # compute numbers, but don't write them out

    #printf("%16s\n","info on mf") > "/dev/stderr"

    for (x in is_group){

        nmf++

        posout[x]=posout[last]+1

	printf("%16s%16s%16s%16s%16s%16s%16s\n", posout[x],0,0,x,0,0,0)

        included[x]=1

        gen[x]=0

        last=x

        cumgen[0]++

	#printf("%10s%16s%10s%16s%10s%10s%10s\n","group",last," included as",posout[x]," as sire, as dam",cum[x,"sire"],cum[x,"dam"]) > "/dev/stderr"

    }

    # regular individuals

#	printf("%16s\n","recoding animals") > "/dev/stderr"

	iter=1

	#--> comment next line and this element of the associative array becomes null

	#printf("%s%16s\n","at the beginning it should be empty: ",posout["00000779770060"]) > "/dev/stderr"

	#-->

	while (changed){

		changed=0

		for (x in pos){

			if(x!=0 && !included[x]){

			# change to number of generation

				#	if(included[dam[x]] && included[sire[x]]){

						if((gen[dam[x]]

							# the new code is actually the order animals are printed

							posout[x]=posout[last]+1

							gen[x]=maxval(gen[dam[x]],gen[sire[x]])+1

							printf("%16s%16s%16s%16s%16s%16s%16s\n", posout[x],posout[dam[x]],posout[sire[x]],x,dam[x],sire[x],gen[x])

							included[x]=1

							changed=1

							last=x

							nanim++

							cumgen[gen[x]]++

						}

				#	}

			}

        	}

		iter++

		#-->

#		printf("%s%16s\n","in the loop: ",posout["00000779770060"]) > "/dev/stderr"

#		fflush("/dev/stderr")

		#-->

		#printf("%10s%10s%10s%10s%16s%16s\n","round",iter,"included",posout[last],"last ",last) > "/dev/stderr"

	}

	#printf("%10s%10s%10s%10s%10s%10s\n","metafounders:",nmf," animals",nanim," total",posout[last]) > "/dev/stderr"

	#printf("%16s%16s\n","pseudogenerations:",gen[last]) > "/dev/stderr"

	    for (x in cumgen){

		#printf("%10s%16s%10s%16s\n","pseudogeneration:",x," including: ",cumgen[x]) > "/dev/stderr"

	    }

	#--> this is the guilty line

#	printf("%s%16s\n","at the end:  ",posout["00000779770060"]) > "/dev/stderr"

#	fflush("/dev/stderr")

	#-->

}