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Changelog

Source: NEWS.md

cpp11bigwig (development version)

cpp11bigwig 0.3.1

CRAN release: 2026-06-26

  • New bigbed_info() and bigwig_info() report header metadata without reading any intervals. bigbed_info() returns the field counts and embedded autoSql schema, making it possible to identify the BED variant a file holds before reading it (a genuine BED12 has defined_field_count == 12). bigwig_info() returns the version, zoom levels, chromosome count, and file-level summary statistics (min/max/mean/std).

  • read_bigbed() now returns all BED columns for files with no embedded autoSql schema (e.g. a bed12 written by bedToBigBed without -as). Previously such files returned only chrom/start/end; the reader now falls back to the field counts in the file header and names columns with the standard BED field names (any extra bedN+ fields become generic fieldN character columns) (#18). When a file has no embedded schema, read_bigbed() now emits a message() noting that the column names were inferred rather than declared by the file; silence it with suppressMessages().

cpp11bigwig 0.3.0

CRAN release: 2026-06-22

  • Fix a CRAN gcc-san (UBSan) load of misaligned address runtime error when reading a bigBed block that packs more than one record. In libBigWig’s bwValues.c, records are stored as three uint32_t fields followed by a variable-length name, so every record after the first starts on an unaligned offset; the fields are now read with memcpy instead of an aligned uint32_t cast.

  • Multi-range queries now open the file once per call instead of re-opening it for every range. The per-range loop moved into C++, so a query of many ranges (and especially a remote file, where each open re-fetches headers) is substantially faster.

  • read_bigbed() no longer crashes on a bigBed file with no embedded autoSql schema. bbGetSQL() returns NULL in that case, and constructing a std::string from it was undefined behavior; such files now read back their chrom/start/end columns with no extra typed fields.

  • The bigWig/bigBed readers now release the libBigWig file handle and read buffer when they error out (e.g. on an unreadable file or a failed interval query), rather than leaking them.

  • Fix a CRAN gcc-ASAN global-buffer-overflow reported when reading bigBed files. The autoSql schema parser no longer uses std::regex (which tripped an AddressSanitizer error inside libstdc++); it now parses the schema with simple string operations.

  • read_bigwig() and read_bigbed() can now query multiple ranges in a single call. Pass equal-length (or length-1, recycled) chrom, start, and end vectors, or a GRanges of regions via chrom. For read_bigwig(as = "Rle"), a multi-range query returns a named RleList with one element per range (#18).

cpp11bigwig 0.2.0

CRAN release: 2026-06-18

  • read_bigwig() gains as = "Rle", returning a per-base run-length-encoded vector spanning the queried range (an Rle for a single chromosome, or a named RleList for several). Uncovered bases are set to the fill value (default 0; use NA to mark them missing) (#18).

  • Fix remote access to large bigWig/bigBed files. The HTTP Range header was not being set, so servers returned the entire file, crashing R or failing to open files larger than the read buffer (#18).

cpp11bigwig 0.1.3

CRAN release: 2025-12-11

  • bigBed columns are now automatically coerced based on autoSql types (#12)

cpp11bigwig 0.1.2

CRAN release: 2025-08-18

  • Fix parsing of bigBed end coordinates.

cpp11bigwig 0.1.1

CRAN release: 2025-01-19

cpp11bigwig 0.1.0

CRAN release: 2025-01-07

  • Initial CRAN submission.

cpp11bigwig 0.0.0.9000

  • libBigWig is mostly untouched excpect for removal of fprintf statements (which R won’t allow in linked libraries) and fixups for ASAN errors, mostly GNU-specific pointer arithmetic. cpp11bigwig passes both ASAN and valgrind checks (via rhub).