Finds subject ranges corresponding to a set of genes (query ranges), taking chromosome into account. Specifically, this function will find the indices of the features (first and last) bounding the ends of a range/gene (start and stop) such that first <= start < stop <= last. Equality is necessary so that multiple conversions between indices and genomic positions will not expand with each conversion. Ranges/genes that are outside the range of feature positions will be given the indices of the corresponding first or last index on that chromosome, rather than 0 or n + 1 so that genes can always be connected to some data. Checking the left and right bound for equality will tell you when a query is off the end of a chromosome.
GRanges or something coercible to GRanges
This function uses some tricks from findIntervals, where is for k queries and n features it is O(k * log(n)) generally and ~O(k) for sorted queries. Therefore will be dramatically faster for sets of query genes that are sorted by start position within each chromosome. The index of the stop position for each gene is found using the left bound from the start of the gene reducing the search space for the stop position somewhat.
This function differs from boundingIndices in that 1. it uses both start and end positions for the subject, and 2. query and subject start and end positions are processed in blocks corresponding to chromosomes.
Both query and subject must be in at least weak genome order (sorted by start within chromosome blocks).
integer matrix with two columns corresponding to indices on left and right bound of queries in subject
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