--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phe/variant_filters/DepthFilter.py	Mon Dec 21 10:50:17 2015 -0500
@@ -0,0 +1,69 @@
+'''Filter VCF on depth of coverage.
+
+Created on 24 Sep 2015
+
+@author: alex
+'''
+import argparse
+import logging
+
+from phe.variant_filters import PHEFilterBase
+
+
+class DepthFilter(PHEFilterBase):
+    """Filter sites by depth."""
+
+    name = "MinDepth"
+    _default_threshold = 5
+    parameter = "min_depth"
+
+    @classmethod
+    def customize_parser(self, parser):
+        arg_name = self.parameter.replace("_", "-")
+        parser.add_argument("--" % arg_name, type=int, default=self._default_threshold,
+                help="Filter sites below minimum depth (default: %s)" % self._default_threshold)
+
+    def __init__(self, args):
+        """Min Depth constructor."""
+        # This needs to happen first, because threshold is initialised here.
+        super(DepthFilter, self).__init__(args)
+
+        # Change the threshold to custom dp value.
+        self.threshold = self._default_threshold
+        if isinstance(args, argparse.Namespace):
+            self.threshold = args.min_depth
+        elif isinstance(args, dict):
+            try:
+                self.threshold = int(args.get(self.parameter))
+            except (TypeError, ValueError):
+                logging.error("Could not retrieve integer threshold from %s", args.get(self.parameter))
+                raise Exception("Could not create depth filter from parameters: %s" % args)
+
+    def __call__(self, record):
+        """Filter a :py:class:`vcf.model._Record`."""
+
+        if len(record.samples) > 1:
+            logging.warn("Currently we only filter VCFs with 1 sample. Only first sample will be used.")
+            logging.warn("This parameter requires to be an integer!")
+
+        try:
+            record_dp = record.samples[0].data.DP
+        except AttributeError:
+            record_dp = None
+
+        if record_dp is None:
+#             logging.debug("Falling back to INFO DP")
+            record_dp = record.INFO.get("DP")
+
+        if record_dp is None or record_dp < self.threshold:
+            return record_dp or False
+        else:
+            return None
+
+    def short_desc(self):
+        short_desc = self.__doc__ or ''
+
+        if short_desc:
+            short_desc = "%s (DP > %i)" % (short_desc, self.threshold)
+
+        return short_desc