Package htsjdk.tribble.index.linear

Class LinearIndex

  • All Implemented Interfaces:
    Index, MutableIndex
    public class LinearIndex
extends AbstractIndex
    Index defined by dividing the genome by chromosome, then each chromosome into bins of fixed width (in genomic coordinates). Features are allocated to bins by start position. The longest feature in each recorded and used to adjust the start position of a query to include all bins that might have a feature that overlaps the query interval. This works well for feature sets of approximately homogeneous length, or whose longest feature is on the order of the bin width or less.

    magicNumber integer type integer version integer filename null terminated character array filesize long lastModified long md5 String flags integer

    ------ LINEAR INDEX nChromosomes integer

    • Field Detail

      • MAX_FEATURES_PER_BIN

        public static final double MAX_FEATURES_PER_BIN

      • INDEX_TYPE

        public static final int INDEX_TYPE

      • enableAdaptiveIndexing

        public static boolean enableAdaptiveIndexing

    • Constructor Detail

      • LinearIndex

        public LinearIndex​(List<LinearIndex.ChrIndex> indices,
                   Path featureFile)
        Initialize using the specified indices
        Parameters:
        indices -
        featureFile -

      • LinearIndex

        public LinearIndex​(List<LinearIndex.ChrIndex> indices,
                   File featureFile)
        Initialize using the specified indices
        Parameters:
        indices -
        featureFile -

      • LinearIndex

        public LinearIndex​(String featureFile)
        Initialize with default parameters
        Parameters:
        featureFile - File for which this is an index

      • LinearIndex

        public LinearIndex​(Path featurePath)
        Initialize with default parameters
        Parameters:
        featurePath - Path for which this is an index

      • LinearIndex

        public LinearIndex​(InputStream inputStream)
            throws IOException
        Load from file.
        Parameters:
        inputStream - This method assumes that the input stream is already buffered as appropriate.
        Throws:
        IOException

    • Method Detail

      • getType

        protected int getType()
        Description copied from class: AbstractIndex
        get the index type
        Specified by:
        getType in class AbstractIndex
        Returns:
        The index type

      • getChrIndexClass

        public Class getChrIndexClass()
        Description copied from class: AbstractIndex
        returns the class for the index type
        Specified by:
        getChrIndexClass in class AbstractIndex
        Returns:
        a Class, from which a new instance can be created

      • optimize

        public Index optimize​(double threshold)
        Adapative optimization of the linear index
        Parameters:
        threshold - threshold to use for optimizing each constituent chrIndex
        Returns:
        The new optimized index

      • optimize

        public Index optimize()

      • writeTable

        public void writeTable​(PrintStream out)
        Code to convert linear index to a text table for analysis
        Parameters:
        out - Stream to which to write out table to

      • setTS

        protected final void setTS​(long ts)