Class DataFrame

A set of DataColumns, indexed by position. This class is used to store data for a chromosome. The DataFrame class manages a collection of data columns, each represented by a DataFrameColumn object. It provides methods to add rows, retrieve rows, and perform various operations on the data. The data is indexed by position using a PosIndex object, and can optionally include reference and alternative alleles. The class also supports creating columns based on VCF header information and resizing the data for memory optimization. The main components of the DataFrame class are: - VariantTypeCounter variantTypeCounter: Keeps track of variant types and their counts. - VariantCategory variantCategory: Represents the category of variants. - int currentIdx: The current index for adding new rows. - PosIndex posIndex: Indexes the data by chromosome position. - StringArray refs: Stores reference alleles. - StringArray alts: Stores alternative alleles. - Mapinvalid input: '<'String, DataFrameColumninvalid input: '<'?>> columns: A map of column names to DataFrameColumn objects. - Fields fields: Represents the fields to create or annotate. The class provides the following key methods: - add(String name, DataFrameColumninvalid input: '<'?> column): Adds a column to the DataFrame. - add(DataFrameRow row): Adds a row to the DataFrame. - check(): Checks the integrity of the data. - columnNames(): Returns an iterable of column names. - createColumn(VcfHeaderInfo vcfHeaderInfo): Creates a column based on VCF header information. - createColumns(): Creates columns based on the fields. - eq(int idx, int pos, String ref, String alt): Checks if the entry at the given index matches the specified position, reference, and alternative alleles. - get(String columnName, int idx): Retrieves data from a column by index. - getColumn(String name): Retrieves a column by name. - getRow(int pos, String ref, String alt): Retrieves a row based on position, reference, and alternative alleles. - find(int pos, String ref, String alt): Finds the index of a row based on position, reference, and alternative alleles. - hasEntry(int pos, String ref, String alt): Checks if an entry exists for the specified position, reference, and alternative alleles. - resize(): Resizes and optimizes the memory usage of the data. - set(String columnName, int idx, Object value): Sets data in a column. - sizeBytes(): Returns the memory size of the DataFrame. - stringArrayMemSize(VariantCategory variantCategory, String field): Calculates the memory size for a string array. - toString(): Returns a string representation of the DataFrame.