added filter_monomorph and filter_callrate flag added

svreader/annotation.py

@@ -204,7 +204,6 @@ class AnnotateReader(VCFReader):
     def getHeader(self):
         return self.vcf_reader.header
 
-
     def add_annotation_metadata(self):
         self.addInfo("SOURCEID", 1, "String",
                      "The source sv identifier")
@@ -520,7 +519,8 @@ def add_filter_infos_header(reader):
     reader.addFilter("ABFREQ", "AB frequency <0.3 for >50% heterosamples")
 
 
-def variant_filtration(SVSet, reader):
+def variant_filtration(variants, reader, filter_monomorph=False,
+                       filter_callrate=False):
     """ Filtering the candidate CNVs according to the following criteria
           - non duplicate sites
           - variant sites
@@ -534,15 +534,15 @@ def variant_filtration(SVSet, reader):
     add_callrate_infos_header(reader)
     add_filter_infos_header(reader)
 
-    for sv in SVSet:
+    for sv in variants:
         info = sv.record.info
         sv.record.info['CALLRATE'] = sv.call_rate(13)
         sv.record.info['VARIANTCALLRATE'] = sv.variant_call_rate(13)
-        if sv.call_rate(13) < 0.75:
+        if sv.call_rate(13) < 0.75 and filter_callrate:
             sv.filter.add("CALLRATE")
-        if not sv.polymorph():
+        if not sv.polymorph() and filter_monomorph:
             sv.filter.add("MONOMORPH")
-        if 'NONDUPLICATEOVERLAP' in info and info['NONDUPLICATEOVERLAP'] > 0.7:
+        if 'NONDUPLICATEOVERLAP' in info and info['NONDUPLICATEOVERLAP'] > 0.8:
             sv.filter.add("OVERLAP")
         if "DUPLICATESCORE" in info is not None and info['DUPLICATESCORE'] > -2:
             sv.filter.add("DUPLICATE")
@@ -559,7 +559,7 @@ def AB_filtering(variant_set):
             if Heterozygote(s):
                 valid_AB_freq.append((s.get('AB')[0] > 0.3))
         if (len(valid_AB_freq) > 0 and
-            sum(valid_AB_freq) < len(valid_AB_freq) / 2):
+                sum(valid_AB_freq) < len(valid_AB_freq) / 2):
             sv.filter.add("ABFREQ")