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#!/usr/local/bin/awk -f
# 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]]<iter) && (gen[sire[x]]<iter)){
# 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")
#-->
}
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