Enum Error 

#[non_exhaustive]
pub enum Error {
    Io(Error),
    Parse {
        line: u64,
        kind: ParseError,
    },
    UnknownFormat {
        hint: String,
    },
    InvalidByte {
        id: String,
        pos: usize,
        byte: u8,
    },
    LengthMismatch {
        id: String,
        seq: usize,
        quality: usize,
    },
    MissingQuality {
        id: String,
    },
    Index(String),
    UnknownSequence(String),
    PairMismatch {
        pairs_read: u64,
        first: String,
        second: String,
    },
    PairTruncated {
        pairs_read: u64,
        missing: &'static str,
    },
    OutOfBounds {
        id: String,
        start: u64,
        end: u64,
        length: u64,
    },
    TooLarge {
        line: u64,
        what: &'static str,
        limit: usize,
    },
    FeatureDisabled(&'static str),
    Unsupported(&'static str),
    Other(String),
}

Everything that can go wrong while reading, writing or indexing sequences.

Marked #[non_exhaustive]: match with a _ arm, so that a future release can describe a new failure without it being a breaking change.

Variants (Non-exhaustive)

Non-exhaustive enums could have additional variants added in future. Therefore, when matching against variants of non-exhaustive enums, an extra wildcard arm must be added to account for any future variants.

Io(Error)

Underlying I/O failure.

Parse

The input is not valid FASTA/FASTQ.

Fields

line: u64

1-based line number on which the problem was detected.

kind: ParseError

What exactly was wrong.

UnknownFormat

The format could not be inferred from a path or from the first bytes.

Fields

hint: String

What was inspected, for the error message.

InvalidByte

A record contains a byte that is not allowed by the requested alphabet.

Fields

id: String

Record identifier, empty if unknown.

pos: usize

Offset of the offending byte inside the sequence.

byte: u8

The offending byte.

LengthMismatch

Sequence and quality strings have different lengths.

Fields

id: String

Record identifier.

seq: usize

Number of residues.

quality: usize

Number of quality characters.

MissingQuality

A FASTQ record was requested but the sequence carries no quality string.

Fields

id: String

Record identifier.

Index(String)

A FASTA index (.fai) is malformed or does not match the FASTA file.

UnknownSequence(String)

A sequence name was not found in a FASTA index.

PairMismatch

Paired reads went out of step: the mate names do not agree.

Fields

pairs_read: u64

How many pairs were read before this one.

first: String

Identifier of the forward read.

second: String

Identifier of the reverse read.

PairTruncated

One of a pair of inputs ended before the other.

Fields

pairs_read: u64

How many complete pairs were read.

missing: &'static str

Which side ran out: "R1", "R2" or "the second mate".

OutOfBounds

A requested region lies outside the sequence.

Fields

id: String

Record identifier.

start: u64

Requested 0-based start.

end: u64

Requested exclusive end.

length: u64

Actual sequence length.

TooLarge

A line or record exceeded a configured size limit.

Only produced when crate::ReaderBuilder::max_line_length or crate::ReaderBuilder::max_record_length is set.

Fields

line: u64

1-based line number at which the limit was hit.

what: &'static str

What grew too large: "line" or "sequence".

limit: usize

The configured limit, in bytes.

FeatureDisabled(&'static str)

The operation requires a cargo feature that was not enabled.

Unsupported(&'static str)

The operation cannot be performed on this input.

Other(String)

A context-specific message, for tools built on top of this library.

Implementations

impl Error

pub fn is_malformed(&self) -> bool

True if the error describes malformed input rather than an I/O failure.

Useful for pipelines that want to skip bad records but abort on a broken pipe.

Trait Implementations

impl Debug for Error

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl Display for Error

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl Error for Error

fn source(&self) -> Option<&(dyn Error + 'static)>

Returns the lower-level source of this error, if any.

fn description(&self) -> &str

👎Deprecated since 1.42.0:

use the Display impl or to_string()

fn cause(&self) -> Option<&dyn Error>

👎Deprecated since 1.33.0:

replaced by Error::source, which can support downcasting

fn provide<'a>(&'a self, request: &mut Request<'a>)

🔬This is a nightly-only experimental API. (error_generic_member_access)

Provides type-based access to context intended for error reports.

impl From<Error> for Error

fn from(e: Error) -> Self

Converts to this type from the input type.

impl From<Error> for Error

fn from(e: Error) -> Self

Converts to this type from the input type.