Class VariantTypeCounters

The VariantTypeCounters class is responsible for counting the number of variants in VCF (Variant Call Format) files. It maintains counters for each chromosome and a counter for all variants combined. The class provides methods to load and save the counters from/to a file, count variants from a VCF file or iterator, and retrieve counters for specific chromosomes. Usage: - Create an instance of VariantTypeCounters with or without specifying Fields and verbosity. - Use the count method to count variants from a VCF file. - Save the counters to a file using the save method. - Load the counters from a file using the static load method. - Retrieve counters for specific chromosomes using the get method. Limitations: - The class assumes that the VCF file is properly formatted and accessible. - The class does not handle multi-threaded access; concurrent modifications may lead to inconsistent state. - The class relies on external classes such as Fields, VariantTypeCounter, VcfFileIterator, VcfEntry, and Log, which are not defined within this class. - The progress display during counting is managed by the ShowProgress class, which is also not defined within this class.