Package 

Class BigFile

  • All Implemented Interfaces:
    java.io.Closeable , java.lang.AutoCloseable 
    
public abstract class BigFile<T extends Object>
 implements Closeable

    A common superclass for Big files.

    Supported format versions

    3 full support 4 partial support, specifically, extra indices aren't supported 5 custom version, requires Snappy instead of DEFLATE for compressed data blocks

    • Method Detail

      • summarize

         final List<BigSummary> summarize(String name, Integer startOffset, Integer endOffset, Integer numBins, Boolean index, Function0<Unit> cancelledChecker)

        Splits the interval [startOffset, endOffset) into numBins non-intersecting sub-intervals (aka bins) and computes a summary of the data values for each bin.

        Parameters:
        name - human-readable chromosome name, e.g.
        startOffset - 0-based start offset (inclusive).
        endOffset - 0-based end offset (exclusive), if 0 than the whole chromosome is used.
        numBins - number of summaries to compute.
        index - if true pre-computed is index is used if possible.
        cancelledChecker - Throw cancelled exception to abort operation

      • query

        @JvmOverloads() final List<T> query(String name, Integer startOffset, Integer endOffset, Boolean overlaps, Function0<Unit> cancelledChecker)

        Queries an R+-tree.

        Parameters:
        name - human-readable chromosome name, e.g.
        startOffset - 0-based start offset (inclusive).
        endOffset - 0-based end offset (exclusive), if 0 than the whole chromosome is used.
        overlaps - if false the resulting list contains only the items completely contained within the query, otherwise it also includes the items overlapping the query.
        cancelledChecker - Throw cancelled exception to abort operation

      • getChromosomes

         final TIntObjectMap<String> getChromosomes()

        An in-memory mapping of chromosome IDs to chromosome names.

        Because sometimes (always) you don't need a B+ tree for that.