jacquard/merge.py
def vcf_records(self, format_tags=None, qualified=False):
        """Generates parsed VcfRecord objects.

        Typically called in a for loop to process each vcf record in a
        VcfReader. VcfReader must be opened in advanced and closed when
        complete. Skips all headers.

        Args:
            qualified: When True, sample names are prefixed with file name

        Returns:
            Parsed VcfRecord

        Raises:
            StopIteration: when reader is exhausted.
            TypeError: if reader is closed.
        """
        if qualified:
            sample_names = self.qualified_sample_names
        else:
            sample_names = self.sample_names

        for line in self._file_reader.read_lines():
            if line.startswith("#"):
                continue
            vcf_record = vcf.VcfRecord.parse_record(line, sample_names)
            if format_tags:
                vcf_record = self.modify_format_tag(vcf_record, format_tags)
            yield vcf_record
def vcf_records(self, format_tags=None, qualified=False):
        """Generates parsed VcfRecord objects.

        Typically called in a for loop to process each vcf record in a
        VcfReader. VcfReader must be opened in advanced and closed when
        complete. Skips all headers.

        Args:
            qualified: When True, sample names are prefixed with file name

        Returns:
            Parsed VcfRecord

        Raises:
            StopIteration: when reader is exhausted.
            TypeError: if reader is closed.
        """
        if qualified:
            sample_names = self.qualified_sample_names
        else:
            sample_names = self.sample_names

        for line in self._file_reader.read_lines():
            if line.startswith("#"):
                continue
            vcf_record = vcf.VcfRecord.parse_record(line, sample_names)
            if format_tags:
                vcf_record = self.modify_format_tag(vcf_record, format_tags)
            yield vcf_record
def vcf_records ( self , format_tags = None , qualified = False ) : if qualified : sample_names = self . qualified_sample_names else : sample_names = self . sample_names for line in self . _file_reader . read_lines ( ) : if line . startswith ( "#" ) : continue vcf_record = vcf . VcfRecord . parse_record ( line , sample_names ) if format_tags : vcf_record = self . modify_format_tag ( vcf_record , format_tags ) yield vcf_record
Generates parsed VcfRecord objects.

        Typically called in a for loop to process each vcf record in a
        VcfReader. VcfReader must be opened in advanced and closed when
        complete. Skips all headers.

        Args:
            qualified: When True, sample names are prefixed with file name

        Returns:
            Parsed VcfRecord

        Raises:
            StopIteration: when reader is exhausted.
            TypeError: if reader is closed.
Generates parsed VcfRecord objects .