NEWS

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superintervalsr 0.99.7

• Use one native genomic index per chromosome with strand filtering in C++.
• Store genomic row IDs and strands as native metadata rather than R objects.
• Update genomic construction and query benchmarks for the shared index.
• Rename the genomic class and constructor to SuperIntervalMap.
• Update overlap methods, conversion, examples and benchmarks to the new name.

superintervalsr 0.99.6

• Root metadata in an R-owned list to avoid expensive per-value preservation and cleanup for large indexes.
• Add SuperIntervalMap, an S4 genomic subject index that preserves source GRanges and supports chromosome-aware and strand-aware overlap methods.
• Return Hits in original input row order and support standard GenomicRanges overlap options, with fallback for zero-width ranges and advanced options.
• Add a real airway RNA-seq annotation workflow and genomic integration tests.
• Validate against R 4.6 and Bioconductor 3.24 development dependencies.

superintervalsr 0.99.5

• Synchronize generated Rcpp bindings and help files with SuperIntervals 1.0.3.
• Correct external-pointer finalizers and preserve metadata per stored occurrence.
• Validate coordinates at construction and mutation, and reject multi-sequence GRanges unless filtered. Keep query paths free of index-state checks.
• Use inclusive coverage widths and widened arithmetic in boundary operations.
• Document sorted indices, reference semantics, metadata policies and genomic coordinate limitations; add executable Bioconductor workflows and regression tests.
• Prepare package metadata, portable C++17 build files and submission guidance.

superintervalsr 0.99.0

• Initial development version of the R wrapper for SuperIntervals.