Annotate uses SVReader

svreader/Annotate.py

 
+
 from svreader import SVRecord, SVReader, SVWriter
 
 from pysam import VariantFile
@@ -7,7 +8,6 @@ HOM_REF = (0, 0)
 HET_VAR = (0, 1)
 HOM_VAR = (1, 1)
 
-
 class AnnotatedRecord(object):
     """
     A lightweight object to annotated the final records
@@ -69,11 +69,14 @@ class AnnotatedRecordSample(object):
 
 class VCFReader(SVReader):
 
-    def __init__(self, file_name, reference_handle=None, svs_to_report=None):
+    def __init__(self, file_name, sv_to_report=None):
         super(VCFReader, self).__init__(file_name,
                                         generic_name,
                                         reference_handle)
         self.vcf_reader = VariantFile(file_name)
+        self.filename = file_name
+        self.sv_to_report =sv_to_report
+        self.vcf_reader = VariantFile(file_name)
 
     def __iter__(self):
         return self
@@ -81,7 +84,7 @@ class VCFReader(SVReader):
     def __next__(self):
         while True:
             raw_record = next(self.vcf_reader)
-            record = AnnotatedRecord(raw_record)
+            record = (raw_record)
             return record
 
     def getHeader(self):
@@ -111,6 +114,7 @@ class VCFReader(SVReader):
 class VCFWriter(SVWriter):
 
     def __init__(self, file_name,  template_reader, index=True):
+
         super(VCFWriter, self).__init__(file_name,
                                         template_reader.tool_name,
                                         template_reader)

svreader/__init__.py

@@ -147,7 +147,7 @@ class SVReader(object):
 
     svs_supported = set(["DEL", "INS", "DUP", "INV"])
 
-    def __init__(self, file_name, tool_name, reference_handle=None):
+    def __init__(self, file_name, tool_name="generic", reference_handle=None):
         self.file_name = file_name
         self.reference_handle = reference_handle
         self.__tool_name = tool_name