correcting a bug in remove_duplicate in __init__

svreader/__init__.py

@@ -223,32 +223,6 @@ class SVReader(object):
 
         return vcf_records
 
-    def RemoveDuplicatePass(self, records, cutoff=1):
-        vcf_records_without_duplicate = []
-        for idx, record in enumerate(records):
-            if self.CheckForDuplicate(idx, record, records, cutoff):
-                vcf_records_without_duplicate.append(record)
-            else:
-                print("removed entry %d %s identified as exact duplicate" %(idx, record))
-        return vcf_records_without_duplicate
-
-    def CheckForDuplicate(self, idx, record, records, cutoff):
-        for test_idx, test_record in enumerate(records):
-                if idx != test_idx:
-                    if record.chrom == test_record.chrom:
-                        if abs(record.start-test_record.start) + abs(record.end-test_record.end) < cutoff:
-                            # We make the assumption that two variants with
-                            # exactly the same breakpoints have the same
-                            # supporting information hence we simply use the
-                            # identifier to distinguish them and keep
-                            # the one with the smaller identifier
-                            if test_idx > idx:
-                                return False
-
-        return True
-
-
-
     def GeneralFilterPass(self, record, minlen, maxlen):
         return (abs(record.sv_len) >= minlen and abs(record.sv_len) <= maxlen)
 
@@ -258,7 +232,7 @@ class SVReader(object):
     def bnd_merge(sef, svtype, records):
         return records  # nothing to do in the majority of cases
 
-    def remove_duplicate(sef, svtype, records):
+    def remove_duplicate(sef, records):
         return records  # nothing to do in the majority of tools (see pindel)