filter_mpile.py does not keep first and last nucleotide in a read

[verku]

The filter_mpile.py script removes (prints “N”) the first nucleotide in the “read” because they are accompanied by “^]” (read start^ and a character for mapping quality). The script also always removes (prints “N”) the last nucleotide in the “read” because they are accompanied by “$” (read end$).