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Exceptions

vartriage.VariantPrioritizationError

Bases: Exception

Base exception for all library errors.

All domain-specific exceptions in this library inherit from this class, making it easy for callers to catch any library error with a single except clause while still allowing fine-grained handling when needed.

Source code in vartriage/io/exceptions.py 
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class VariantPrioritizationError(Exception):
    """Base exception for all library errors.

    All domain-specific exceptions in this library inherit from
    this class, making it easy for callers to catch any library
    error with a single except clause while still allowing
    fine-grained handling when needed.
    """

vartriage.ParseError

Bases: VariantPrioritizationError

Raised when VCF content cannot be parsed.

Covers both header-level violations (missing ##fileformat declaration, malformed ##INFO/##FORMAT meta-information lines, absent #CHROM column header) and data-line violations (missing mandatory columns, invalid field values).

Parameters

line_number : int 1-based line number in the source file where the error occurred. detail : str Human-readable description of the parse failure. field : str, optional Name of the specific VCF field that failed validation (e.g., "QUAL", "POS"). None when the error is not tied to a single field (e.g., a missing column header line).

Attributes

line_number : int 1-based line number where the error occurred. field : Optional[str] Name of the field that failed validation, or None. detail : str Human-readable description of the parse failure.

Examples

raise ParseError( ... line_number=5, ... detail="Missing mandatory QUAL column", ... ) Traceback (most recent call last): ... ParseError: Line 5: Missing mandatory QUAL column

raise ParseError( ... line_number=12, ... field="POS", ... detail="Non-integer value 'abc'", ... ) Traceback (most recent call last): ... ParseError: Line 12, field 'POS': Non-integer value 'abc'

Source code in vartriage/io/exceptions.py 
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class ParseError(VariantPrioritizationError):
    """Raised when VCF content cannot be parsed.

    Covers both header-level violations (missing ``##fileformat``
    declaration, malformed ``##INFO``/``##FORMAT`` meta-information
    lines, absent ``#CHROM`` column header) and data-line violations
    (missing mandatory columns, invalid field values).

    Parameters
    ----------
    line_number : int
        1-based line number in the source file where the error
        occurred.
    detail : str
        Human-readable description of the parse failure.
    field : str, optional
        Name of the specific VCF field that failed validation
        (e.g., ``"QUAL"``, ``"POS"``). ``None`` when the error
        is not tied to a single field (e.g., a missing column
        header line).

    Attributes
    ----------
    line_number : int
        1-based line number where the error occurred.
    field : Optional[str]
        Name of the field that failed validation, or ``None``.
    detail : str
        Human-readable description of the parse failure.

    Examples
    --------
    >>> raise ParseError(
    ...     line_number=5,
    ...     detail="Missing mandatory QUAL column",
    ... )
    Traceback (most recent call last):
        ...
    ParseError: Line 5: Missing mandatory QUAL column

    >>> raise ParseError(
    ...     line_number=12,
    ...     field="POS",
    ...     detail="Non-integer value 'abc'",
    ... )
    Traceback (most recent call last):
        ...
    ParseError: Line 12, field 'POS': Non-integer value 'abc'
    """

    def __init__(
        self,
        line_number: int,
        detail: str,
        field: str | None = None,
    ) -> None:
        self.line_number: int = line_number
        self.field: str | None = field
        self.detail: str = detail

        if field is not None:
            message = f"Line {line_number}, field '{field}': {detail}"
        else:
            message = f"Line {line_number}: {detail}"

        super().__init__(message)

vartriage.ConfigurationError

Bases: VariantPrioritizationError

Raised when pipeline configuration is invalid.

Thrown during configuration construction or pipeline initialization when a parameter value falls outside its permitted range or a required value is absent. The exception message names the invalid parameter and describes the valid range or format.

Examples

raise ConfigurationError( ... "min_qual must be between 0 and 1000000, got -5" ... ) Traceback (most recent call last): ... ConfigurationError: min_qual must be between 0 and 1000000...

Source code in vartriage/io/exceptions.py 
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class ConfigurationError(VariantPrioritizationError):
    """Raised when pipeline configuration is invalid.

    Thrown during configuration construction or pipeline
    initialization when a parameter value falls outside its
    permitted range or a required value is absent. The exception
    message names the invalid parameter and describes the valid
    range or format.

    Examples
    --------
    >>> raise ConfigurationError(
    ...     "min_qual must be between 0 and 1000000, got -5"
    ... )
    Traceback (most recent call last):
        ...
    ConfigurationError: min_qual must be between 0 and 1000000...
    """

vartriage.ReferenceFileError

Bases: VariantPrioritizationError

Raised when a reference file cannot be loaded or parsed.

Thrown when the annotation or prioritization engine is unable to open, read, or parse a reference data file (gnomAD, ClinVar, GTF/GFF gene annotation, CADD scores, REVEL scores). The exception message includes the file path and a description of the failure so the caller can distinguish a missing file from a format error.

Examples

raise ReferenceFileError( ... "/data/gnomad.vcf.gz: file not found" ... ) Traceback (most recent call last): ... ReferenceFileError: /data/gnomad.vcf.gz: file not found

Source code in vartriage/io/exceptions.py 
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class ReferenceFileError(VariantPrioritizationError):
    """Raised when a reference file cannot be loaded or parsed.

    Thrown when the annotation or prioritization engine is unable
    to open, read, or parse a reference data file (gnomAD, ClinVar,
    GTF/GFF gene annotation, CADD scores, REVEL scores). The
    exception message includes the file path and a description of
    the failure so the caller can distinguish a missing file from a
    format error.

    Examples
    --------
    >>> raise ReferenceFileError(
    ...     "/data/gnomad.vcf.gz: file not found"
    ... )
    Traceback (most recent call last):
        ...
    ReferenceFileError: /data/gnomad.vcf.gz: file not found
    """