diff --git a/svreader/Annotate.py b/svreader/Annotate.py index 56fe661029971e48a3cb6f5c9ba9bc788fadd5f1..d6bb22af15cd5ce9d79c3b183e57cbfccf4a1647 100644 --- a/svreader/Annotate.py +++ b/svreader/Annotate.py @@ -1,4 +1,5 @@ + 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) diff --git a/svreader/__init__.py b/svreader/__init__.py index f9482a5cf90ef79eed57abddf704a2783f698b48..be3e22ca439d4c2d8482d0019de18dc7ad5e2cb7 100644 --- a/svreader/__init__.py +++ b/svreader/__init__.py @@ -147,7 +147,7 @@ class SVReader(object): svs_supported = set(["DEL", "INS", "DUP", "INV"]) - def __init__(self, file_name, tool_name="default", 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