bash variable created with awk moves in echo output - bash

Question

my while loop is reading a file that looks like:
Chr start stop value
chr1 12345 4345666 -1
to compare with another file to create mean values of those values (probes.txt):
chr1 12345 12345 0.124
chr1 12346 12346 0.421
now the code goes:
$file | while read line
do
first=$(echo $line | awk '{print $1}' )
second=$(echo $line | awk '{print $2}')
third=$(echo $line | awk '{print $3}')
logsum=$(awk -v first=$first -v second=$second -v third=$third '$1==first && $2>= second && $3<=third { sum += $4; n++} END { print sum / n; }' probes.txt
echo "$line" "$logsum"
done
the output that I am expecting would be:
chr1 12345 4345666 -1 0.232
but instead the $logsum ends up at the front overriding parts of the $line:
0.232345 4345666 -1 0.232
i have also tried printf and get the same issue with
printf "%s %s \n" "$line" "$logsum"
i think the problem is the $logsum variable as it seems ok if I
echo "$logsum" "$line"
instead.
Does anyone know what is happening here and how to fix it?
edit I am working on a Mac in case this is an issue
fixed with dos2unix

Answer 1

Apart from checking for \r\n characters, as suggested by #kvantour, I'd recommend to do all of this in a single AWK script. This will be more efficient.
Let's say, if you save this to script.awk:
NR == 1 { print $0,"logsum"; next }
{
sum = 0; n = 0; avg = 0;
while(( getline line < fn) > 0) {
split(line, arr);
if (arr[1]==$1 && arr[2]>=$2 && arr[3]<=$3) {
sum += arr[4]; n++;
}
}
if (n>0) avg = (sum / n);
print $0, avg;
}
You can call it like this:
awk -v fn=probes.txt -f script.awk YOURFILE.txt
Example output:
Chr start stop value logsum
chr1 12345 4345666 -1 0.2725