Genotype API Documentation - v0.1.0
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    Interface FastqSequence

    FASTQ sequence with quality scores and statistics Format:

    description\nsequence\n+\nquality

    Extends both AbstractSequence (for the operations pipeline) and QualityScoreBearing (for quality-aware operations shared with alignment records). The stats field is carried over from FASTXSequence for backward compatibility.

    interface FastqSequence {
        id: string;
        description?: string;
        sequence: GenotypeString;
        length: number;
        lineNumber?: number;
        quality: GenotypeString;
        qualityEncoding: QualityEncoding;
        format: "fastq";
        stats?: {
            length: number;
            gcContent?: number;
            hasAmbiguousBases?: boolean;
            hasGaps?: boolean;
            hasLowQuality?: boolean;
        };
        qualityScores?: number[];
        qualityStats?: {
            mean: number;
            min: number;
            max: number;
            lowQualityBases: number;
        };
    }

    Hierarchy (View Summary)

    Index

    Properties

    id description? sequence length lineNumber? quality qualityEncoding format stats? qualityScores? qualityStats?

    Properties

    id: string

    Sequence identifier (required, but may be empty string in malformed data)

    description?: string

    Optional description/comment line

    sequence: GenotypeString

    The actual sequence data

    length: number

    Cached sequence length for performance

    lineNumber?: number

    Original line number where this sequence started (for error reporting)

    quality: GenotypeString
    qualityEncoding: QualityEncoding
    format: "fastq"
    stats?: {
        length: number;
        gcContent?: number;
        hasAmbiguousBases?: boolean;
        hasGaps?: boolean;
        hasLowQuality?: boolean;
    }

    Computed sequence statistics

    qualityScores?: number[]

    Parsed numeric quality scores (lazy-loaded)

    qualityStats?: {
        mean: number;
        min: number;
        max: number;
        lowQualityBases: number;
    }

    Computed quality statistics

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