awk -v m=50 '    # set maximum distance for difference and store as variable m
  NR==FNR {      # For each line in the 1st input file (file2)...
    for(i=4; i<=NF; i++) {   # start at field 4 and store in i as a loop (capture variable fields lenght of each line)
      split($i,F,/-/)   # split each i on the - (hyphen)
      L[$2,i-3]=F[1]    # store the left of the - as F[1]
      R[$2,i-3]=F[2]    # store the right of the - asF[2}
    }    # end file2 processing
    if(NF>n)
      n=NF
    next
  } 
  $9=="." && $12=="." {   # only look at lines where fields 9 and 12 have a . (dot) in file1
    d=">50" 
    for(i=1; i<=n; i++) {   # create loop for file1 i variable
      if( ($8,i) in L) {    # loop hrough field 8 of file1 and store in variable L
        if((d1=$4-L[$8,i])<0)
          d1=-d1 
        if((d2=$4-R[$8,i])<0)
          d2=-d2 
        if(d1<=50 || d2<=50) {
          if(d1<=50 && d2<=50) {
            if(d1<d2)
              d=-d1
            else
              d=d2
          }
          else {
            if(d1<=50)
              d=-d1
            else
              d=d2
          }
          break     # break out of this for loop.
        }
      }
    }
    $9=d
  }
  1    
' file2 FS='\t' OFS='\t' file1   # End the awk script and name the input files to be processed with field seperators set as tab.