1 files changed, 99 insertions, 0 deletions
diff --git a/test/arrayind1.awk b/test/arrayind1.awk
new file mode 100755
index 00000000..29fe80bc
--- /dev/null
+++ b/test/arrayind1.awk
@@ -0,0 +1,99 @@
+#!/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"
+		#-->
+		#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"
+	#-->
+}