CHANGES 
-----------------------
* 2026-10-07
  RbowtieCuda version 1.4.4

  - nvBowtie: faster paired-end opposite-mate scoring using a Myers bit-vector core, enabled by
    default; use --opposite-myers 0 to restore the previous algorithm. Alignment output is
    unchanged (bit-identical SAM records); the scoring stage is ~1.7x faster on GPU.
  - CUDA architectures are auto-detected at build time (native code for the installed GPUs, with a
    PTX fallback), replacing the previously hard-coded target.
  - Faster host/GPU transfers through page-locked buffers and stream-scoped synchronisation.
  - Faster BWT occurrence-table construction on CPU.

  
* 2026-05-08
  RbowtieCuda version 1.4.3

  - Fix for an issue with the Thrust library

* 2026-04-10
  RbowtieCuda version 1.0.11

  - Installation modifications


* 2025-10-12
  RbowtieCuda version 1.0.10

  - Installation modifications


* 2025-09-25
  RbowtieCuda version 1.0.9

  - nvBowtie, nvBWT and nvbio_test propagate their error messages to the R interface
  - Improved diagnostic messages during package installation
  - Improved program stability
  - Faster startup
  - Compatible with CUDA 13.0
  - The program needs 16 GB of RAM to be compiled (with Sys.setenv(MAKEFLAGS="-j8"))


* 2025-04-17
  RbowtieCuda version 1.0.1

  - The package is available on Bioconductor






