Genotype API Documentation - v0.1.0
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    Interface SubseqOptions

    Configuration options for subsequence extraction

    Provides flexible ways to specify regions to extract, including simple coordinates, region files, and flanking sequences.

    interface SubseqOptions {
        region?: string;
        regions?: string[];
        start?: number;
        end?: number;
        bedFile?: string;
        bedRegions?: { chromosome: string; chromStart: number; chromEnd: number }[];
        gtfFile?: string;
        gtfFeatures?: {
            seqname: string;
            start: number;
            end: number;
            feature: string;
        }[];
        featureType?: string;
        idPattern?: RegExp;
        idList?: string[];
        upstream?: number;
        downstream?: number;
        onlyFlank?: boolean;
        oneBased?: boolean;
        strand?: "+"
        | "-"
        | "both";
        reverseComplementMinus?: boolean;
        circular?: boolean;
        includeCoordinates?: boolean;
        coordinateSeparator?: string;
        concatenate?: boolean;
    }
    Index

    Properties

    region? regions? start? end? bedFile? bedRegions? gtfFile? gtfFeatures? featureType? idPattern? idList? upstream? downstream? onlyFlank? oneBased? strand? reverseComplementMinus? circular? includeCoordinates? coordinateSeparator? concatenate?

    Properties

    region?: string

    Single region string like "1:100", "50:-1", "-100:-1"

    regions?: string[]

    Multiple region strings

    start?: number

    Start position (alternative to region)

    end?: number

    End position (alternative to region)

    bedFile?: string

    BED file path to load regions from

    bedRegions?: { chromosome: string; chromStart: number; chromEnd: number }[]

    BED regions to extract (alternative to bedFile)

    gtfFile?: string

    GTF file path to load features from

    gtfFeatures?: { seqname: string; start: number; end: number; feature: string }[]

    GTF features to extract (alternative to gtfFile)

    featureType?: string

    Feature type to filter (for GTF)

    idPattern?: RegExp

    Pattern to match sequence IDs

    idList?: string[]

    List of sequence IDs to extract

    upstream?: number

    Number of bases to include upstream of region

    downstream?: number

    Number of bases to include downstream of region

    onlyFlank?: boolean

    Extract only flanking sequences, not the region itself

    oneBased?: boolean

    Use 1-based coordinates (default: true for biological convention)

    strand?: "+" | "-" | "both"

    Strand orientation for extraction

    reverseComplementMinus?: boolean

    Reverse complement if on minus strand

    circular?: boolean

    Treat sequences as circular

    includeCoordinates?: boolean

    Include region coordinates in sequence ID

    coordinateSeparator?: string

    Separator for coordinate suffix in ID

    concatenate?: boolean

    Concatenate multiple regions

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