more pep8 compliance

svreader/annotation.py

@@ -178,7 +178,7 @@ class AnnotateRecord(VCFRecord):
         filters = [f for f in record.filter]
         # We make the assumption when a "." is present no other filter
         # are present
-        if len(filters) == 0 or "." in filters:
+        if not filters or "." in filters:
             record.filter.clear()
             record.filter.add("PASS")
 
@@ -416,7 +416,9 @@ def add_redundancy_infos_header(reader):
 
 
 def redundancy_annotator(SVSet, reader,
-                          duplicatescore_threshold=-2, genotyper="svtyper"):
+                         overlap_cutoff,
+                         duplicatescore_threshold=-2,
+                         genotyper="svtyper"):
     """ Annotating duplicate candidates based on the genotype likelihoods
       - genotype likelihoods can be provided by svtyper or genomestrip
     """
@@ -430,7 +432,7 @@ def redundancy_annotator(SVSet, reader,
 
     pybed_variants = vcf_to_pybed(SVSet)
     self_overlap = pybed_variants.intersect(pybed_variants,
-                                            f=0.5, r=True, wo=True)
+                                            f=overlap_cutoff, r=True, wo=True)
 
     seen = defaultdict(tuple)
     duplicates = defaultdict(list)
@@ -519,7 +521,7 @@ def add_filter_infos_header(reader):
     reader.addFilter("ABFREQ", "AB frequency <0.3 for >50% heterosamples")
 
 
-def variant_filtration(variants, reader, filter_monomorph=False,
+def variant_filtration(variant_set, reader, filter_monomorph=False,
                        filter_callrate=False):
     """ Filtering the candidate CNVs according to the following criteria
           - non duplicate sites
@@ -534,7 +536,7 @@ def variant_filtration(variants, reader, filter_monomorph=False,
     add_callrate_infos_header(reader)
     add_filter_infos_header(reader)
 
-    for sv in variants:
+    for sv in variant_set:
         info = sv.record.info
         sv.record.info['CALLRATE'] = sv.call_rate(13)
         sv.record.info['VARIANTCALLRATE'] = sv.variant_call_rate(13)
@@ -563,14 +565,14 @@ def AB_filtering(variant_set):
             sv.filter.add("ABFREQ")
 
 
-def get_connected_duplicates(SVSet):
+def get_connected_duplicates(variant_set):
     """
     Construct connected components of duplicates and rename the variants
     """
     undirected = Graph()
     variant_dict = defaultdict()
     representatives = defaultdict()
-    for s in SVSet:
+    for s in variant_set:
         variant_dict[s.id] = s
         if "DUPLICATE" in s.filter:
             for dupli_repr in s.record.info["DUPLICATEOF"]:
@@ -604,8 +606,8 @@ def get_tool_name(sv_ident):
     return sv_ident.split("_")[0]
 
 
-def set_supporting_tools(SVSet):
-    for sv in SVSet:
+def set_supporting_tools(variant_set):
+    for sv in variant_set:
         tools = {get_tool_name(sv.id)}
         if "DUPLICATES" in sv.record.info:
             duplicates = sv.record.info['DUPLICATES']