for file in /home/cmccabe/Desktop/concordance/comparison/update/*.txt ; do
    file1=${file##*/}    # Strip off directory
    getprefix=${file1%%_*.txt}
    file1=$(printf '%s\n' "/home/cmccabe/Desktop/concordance/reference/files/${file1%%_*.txt}_"*.txt) # look for matching file
    if [[ -f "$file1" ]]
    then
          awk '
BEGIN {FS = OFS = "\t"
}
NR == 1 {
outfile = FILENAME
}
FNR == NR {
o[i[++ic] = $1 OFS $2 OFS $3] = $0
}
{for(i=1;i<=19;i++)
{if(!$i){$i="."}}
}
{if($2 OFS $4 OFS $5 in o)
o[$2 OFS $4 OFS $5] = $1 OFS $2 OFS $4 OFS $5 OFS $6 OFS $7 OFS $8 OFS $9 OFS $10 OFS $11 OFS $12 OFS $13 OFS $14 OFS $15 OFS $16 OFS $17 OFS $18 OFS $19           }   
END {for(j = 1; j <= ic; j++)
print o[i[j]] > outfile
}' $file $file1
   fi
done