Merge pull request #13554 from mvdbeek/fix_sff_extractor_tool

import subprocess

import sys

import tempfile

from typing import Dict, List

__author__ = 'Jose Blanca and Bastien Chevreux'

__copyright__ = 'Copyright 2008, Jose Blanca, COMAV, and Bastien Chevreux'

fake_sff_name = 'fake_sff_name'

# readname as key: lines with matches from SSAHA, one best match

ssahapematches: Dict[str, List] = {}

ssahapematches = {}  # type: ignore

# linker readname as key: length of linker sequence

linkerlengths: Dict[str, int] = {}

linkerlengths = {}  # type: ignore

# set to true if something really fishy is going on with the sequences

stern_warning = True

    </help>

</tool>