varlociraptor 5.6.1

use bio_types::genome::Locus;
use std::path::PathBuf;

use thiserror::Error;

#[derive(Error, Debug, PartialEq)]
pub(crate) enum Error {
    #[error("formula refers to unknown sample {name}")]
    InvalidSampleName { name: String },
    #[error("contamination refers to unknown sample {name}; it is not defined in the scenario")]
    InvalidContaminationSampleName { name: String },
    #[error(
        "inheritance definition refers to unknown sample {name}; it is not defined in the scenario"
    )]
    InvalidInheritanceSampleName { name: String },
    #[error("observation files must be provided as samplename=path")]
    InvalidObservationsSpec,
    #[error(
        "invalid variant index given, must be not higher than the number of variants at the locus"
    )]
    InvalidIndex,
    #[error("invalid locus for --testcase-locus. Use CHROM:POS syntax")]
    InvalidLocus,
    #[error("no candidate variant at the given locus")]
    NoCandidateFound,
    #[error("testcase prefix must be given with --testcase-prefix")]
    MissingPrefix,
    #[error("expected tag {name} missing from BCF record")]
    MissingBCFTag { name: String },
    #[error("invalid BCF record at {chrom}:{pos}: {msg}")]
    InvalidBCFRecord {
        chrom: String,
        pos: i64,
        msg: String,
    },
    #[error("unable to estimate TMB because no valid records were found in the given BCF/VCF")]
    NoRecordsFound,
    #[error("contig {contig} not found in universe definition and no 'all' defined")]
    UniverseContigNotFound { contig: String },
    #[error("contig {contig} not found in ploidy definition and no 'all' defined")]
    PloidyContigNotFound { contig: String },
    #[error("record {i} in candidate BCF/VCF does not define a chromosome")]
    RecordMissingChrom { i: usize },
    #[error("inconsistent observations: input observation BCF files do not contain exactly the same records")]
    InconsistentObservations,
    #[error("sample {name} (given by --obs) cannot be found in the scenario")]
    InvalidObservationSampleName { name: String },
    #[error("invalid observations: varlociraptor cannot be parsed from given observations ({path}); either the file has not been preprocessed with varlociraptor or with a too old version")]
    InvalidObservations { path: PathBuf },
    #[error("invalid observations: varlociraptor cannot read given observations; either the file has not been preprocessed with varlociraptor or with a too old version")]
    InvalidObservationFormat,
    #[error("invalid BND record: ALT {spec} does not follow BND spec")]
    InvalidBNDRecordAlt { spec: String },
    #[error("at least one BCF with observations must be provided")]
    EmptyObservations,
    #[error(
        "undefined expression {identifier}; please define under 'expressions:' in your scenario"
    )]
    UndefinedExpression { identifier: String },
    #[error("invalid prior configuration: {msg}")]
    InvalidPriorConfiguration { msg: String },
    #[error("read position determined from cigar string exceeds record length")]
    ReadPosOutOfBounds,
    #[error("invalid strand information '{value}', must be '+', '-', '*' or '.'")]
    InvalidStrandInfo { value: char },
    #[error("invalid read orientation information '{value}', must be 'F1R2', 'F2R1', etc.")]
    InvalidReadOrientationInfo { value: String },
    #[error("the following events are not disjunct: {expressions}")]
    OverlappingEvents { expressions: String },
    #[error("the input VCF/BCF is not sorted: {previous_locus:?} > {current_locus:?}")]
    UnsortedVariantFile {
        previous_locus: Locus,
        current_locus: Locus,
    },
    // #[error("invalid phase set, PS tag only supported for single sample VCF/BCF, may only contain a single value, and records may only contain a single ALT allele")]
    // InvalidPhaseSet,
    #[error("haplotype block consisting of normal variants in combination with breakends: this is currently unsupported")]
    HaplotypeBlockWithBreakend,
    #[error("invalid prior contamination estimate. Both --prior-estiate and --prior-considered-cells have to be specified. The latter has to be >0.")]
    InvalidPriorContaminationEstimate,
    #[error("breakend with MATEID found that does not have its own ID set: this is currently unsupported, as there is no way to uniquely identify the pair")]
    BreakendMateidWithoutRecid,
}

pub(crate) fn invalid_bcf_record(chrom: &str, pos: i64, msg: &str) -> Error {
    Error::InvalidBCFRecord {
        chrom: chrom.to_owned(),
        pos,
        msg: msg.to_owned(),
    }
}