cpp11bigwig 0.3.0

• 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

• 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

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

cpp11bigwig 0.1.2

• Fix parsing of bigBed end coordinates.

cpp11bigwig 0.1.1

• Sync with libBigWig v0.4.8

cpp11bigwig 0.1.0

• 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).