jacquard/variant_caller_transforms/varscan.py
def claim(self, file_readers):
        """Recognizes and claims VarScan VCFs form the set of all input VCFs.

        Each defined caller has a chance to evaluate and claim all the incoming
        files as something that it can process. Since VarScan can claim
        high-confidence files as well, this process is significantly more
        complex than for other callers.

        Args:
            file_readers: the collection of currently unclaimed files

        Returns:
            A tuple of unclaimed readers and VarScanVcfReaders.
        """

        (prefix_to_readers,
         filter_files,
         unclaimed_set) = self._find_varscan_files(file_readers)

        prefix_by_patients = self._split_prefix_by_patient(prefix_to_readers)
        self._validate_vcf_readers(prefix_by_patients)
        vcf_hc_pairs = self._pair_files(prefix_to_readers, filter_files)
        self._validate_vcf_hc_pairs(vcf_hc_pairs)
        vcf_readers = self._create_vcf_readers(vcf_hc_pairs)

        return list(unclaimed_set), vcf_readers
def claim(self, file_readers):
        """Recognizes and claims VarScan VCFs form the set of all input VCFs.

        Each defined caller has a chance to evaluate and claim all the incoming
        files as something that it can process. Since VarScan can claim
        high-confidence files as well, this process is significantly more
        complex than for other callers.

        Args:
            file_readers: the collection of currently unclaimed files

        Returns:
            A tuple of unclaimed readers and VarScanVcfReaders.
        """

        (prefix_to_readers,
         filter_files,
         unclaimed_set) = self._find_varscan_files(file_readers)

        prefix_by_patients = self._split_prefix_by_patient(prefix_to_readers)
        self._validate_vcf_readers(prefix_by_patients)
        vcf_hc_pairs = self._pair_files(prefix_to_readers, filter_files)
        self._validate_vcf_hc_pairs(vcf_hc_pairs)
        vcf_readers = self._create_vcf_readers(vcf_hc_pairs)

        return list(unclaimed_set), vcf_readers
Recognizes and claims VarScan VCFs form the set of all input VCFs.

        Each defined caller has a chance to evaluate and claim all the incoming
        files as something that it can process. Since VarScan can claim
        high-confidence files as well, this process is significantly more
        complex than for other callers.

        Args:
            file_readers: the collection of currently unclaimed files

        Returns:
            A tuple of unclaimed readers and VarScanVcfReaders.