Package htsjdk.tribble.example

Class CountRecords

  • public class CountRecords
extends Object
    An example of how to index a feature file, and then count all the records in the file. This is also useful for testing the feature reader

    • Constructor Detail

      • CountRecords

        public CountRecords()

    • Method Detail

      • main

        public static void main​(String[] args)
        The main method of this class: 1) checks to see that the feature file exists 2) loads an index from disk, if one doesn't exist, it creates it and writes it to disk 3) creates a FeatureSource 4) iterates over the records, emitting a final tally for the number of features seen
        Parameters:
        args - a single parameter, the file name to load

      • runWithIndex

        public static long runWithIndex​(File featureInput,
                                FeatureCodec codec,
                                int optimizeThreshold)
        Parameters:
        featureInput - File containing features
        codec - Codec used to read the features
        optimizeThreshold - Threshold used to optimize the linear index
        Returns:
        See Also:
        LinearIndex.optimize(double)

      • printUsage

        public static void printUsage()
        print usage information

      • loadIndex

        public static Index loadIndex​(File featureFile,
                              FeatureCodec codec)
        Parameters:
        featureFile - the feature file
        codec - the codec to decode features with
        Returns:
        an index instance

      • createAndWriteNewIndex

        public static Index createAndWriteNewIndex​(File featureFile,
                                           File indexFile,
                                           FeatureCodec codec)
        creates a new index, given the feature file and the codec
        Parameters:
        featureFile - the feature file (i.e. .vcf, .bed)
        indexFile - the index file; the location we should be writing the index to
        codec - the codec to read features with
        Returns:
        an index instance

      • getFeatureCodec

        public static FeatureCodec getFeatureCodec​(File featureFile)
        Return a FeatureCodec instance appropriate for the given featureFile. Codec is generated based on file extension
        Parameters:
        featureFile -
        Returns:
        Throws:
        IllegalArgumentException - If a codec cannot be found