Variable SAMUtilsConst

Type Declaration

• detectFormat: function

  • detectFormat(data: string): boolean

    Detect if string contains SAM format data

    Parameters

    • data: string

    Returns boolean

• decodeFlag: function

  • decodeFlag(
        flag: number,
    ): {
        isPaired: boolean;
        isProperPair: boolean;
        isUnmapped: boolean;
        isMateUnmapped: boolean;
        isReverse: boolean;
        isMateReverse: boolean;
        isFirstInPair: boolean;
        isSecondInPair: boolean;
        isSecondary: boolean;
        isQCFail: boolean;
        isDuplicate: boolean;
        isSupplementary: boolean;
    }

    Decode SAM flag into human-readable components

    Parameters

    • flag: number

    Returns {
        isPaired: boolean;
        isProperPair: boolean;
        isUnmapped: boolean;
        isMateUnmapped: boolean;
        isReverse: boolean;
        isMateReverse: boolean;
        isFirstInPair: boolean;
        isSecondInPair: boolean;
        isSecondary: boolean;
        isQCFail: boolean;
        isDuplicate: boolean;
        isSupplementary: boolean;
    }

• parseCIGAROperations: function

  • parseCIGAROperations(cigar: string): { operation: string; length: number }[]

    Parse CIGAR string into operations

    Parameters

    • cigar: string

    Returns { operation: string; length: number }[]

• calculateReferenceSpan: function

  • calculateReferenceSpan(cigar: string): number

    Calculate alignment span on reference

    Parameters

    • cigar: string

    Returns number