Given a query set of genome intervals, identify the genes whose transcription start site is within a specified distance
GRanges object of intervals to query
GRanges object of gene locations with TSS window pre-computed
matrix where rows correspond to queries, and columns correspond to genes. If query i overlaps gene j, then M[i,j] = 1. All other entries are zero, so a sparse matrix is used to reduce memory usage.
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