--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phe/variant_filters/MQ0FFilter.py	Mon Dec 21 10:50:17 2015 -0500
@@ -0,0 +1,64 @@
+'''Filter VCF on MQ filter.
+Created on 24 Sep 2015
+
+@author: alex
+'''
+
+import argparse
+import logging
+
+from phe.variant_filters import PHEFilterBase
+
+
+class MQ0FFilter(PHEFilterBase):
+    '''Filter sites by MQ0F (Total Mapping Quality Zero Reads to DP) ratio.'''
+
+    name = "MinMQ0F"
+    _default_threshold = 0.05
+    parameter = "mq0f_ratio"
+
+    @classmethod
+    def customize_parser(self, parser):
+        arg_name = self.parameter.replace("_", "-")
+        parser.add_argument("--%s" % arg_name, type=float, default=self._default_threshold,
+                help="Filter sites below given MQ0F ratio (default: %s)" % self._default_threshold)
+
+    def __init__(self, args):
+        """Min Mapping Quality Zero constructor."""
+        # This needs to happen first, because threshold is initialised here.
+        super(MQ0FFilter, self).__init__(args)
+
+        # Change the threshold to custom gq value.
+        self.threshold = self._default_threshold
+        if isinstance(args, argparse.Namespace):
+            self.threshold = args.mq_score
+        elif isinstance(args, dict):
+            try:
+                self.threshold = float(args.get(self.parameter))
+            except (TypeError, ValueError):
+                logging.error("Could not retrieve threshold from %s", args.get(self.parameter))
+                logging.error("This parameter requires to be a float!")
+                raise Exception("Could not create MQ0F filter from parameters: %s" % args)
+
+    def __call__(self, record):
+        """Filter a :py:class:`vcf.model._Record`."""
+
+        good_record = self._check_record(record)
+
+        if good_record is not True:
+            return good_record
+        record_mq = record.INFO.get("MQ0F")
+
+        if record_mq is None or record_mq > self.threshold:
+            # FIXME: when record_mq is None, i,e, error/missing, what do you do?
+            return record_mq or False
+        else:
+            return None
+
+    def short_desc(self):
+        short_desc = self.__doc__ or ''
+
+        if short_desc:
+            short_desc = "%s (MQ0F > %s)" % (short_desc, self.threshold)
+
+        return short_desc