v2.4.0

* Fixed an issue in BAM pattern source where one thread would prematurely
  close the read file pointer resulting in other threads crashing because
  of "Bad file descriptor" errors.
* Fixed an issue that would cause bowtie2 to crash with `--no-1mm-upfront`
  specified
* Modified bowtie2-build script to better handle of flags and positional
  parameters
* Migrated all python scripts to python3.
* Added support for wildcards in input files to bowtie2 wrapper script e.g.
  `bowtie2 -x index -q *.fq as opposed to bowtie2 -x index -q 1.fq,2.fq,3.fq...`
* Fixed an issue causing bowtie2 to incorrectly process read names see
  [#265](https://github.com/BenLangmead/bowtie2/issues/265)
* Added support for allowing presets to be overridden by more specific
  options e.g `bowtie2 -x index --local --very-fast-local --L22 -q reads.fq`
  will cause bowtie2 to use a seed length of 22 instead of a seed length
  of 25 that's configured for `--very-fast-local` preset.
* Modified SAM output for `-k`/`-a` so that supplementary alignments get
  assigned a MAPQ of 255.
* Fixed an issue that would cause bowtie2-build to not generate
  reverse index files.
* Added preliminary support for ppc64le architectures with the help of
  SIMDE project see [#271](https://github.com/BenLangmead/bowtie2/issues/271) for details.
* Fixed an issue causing bowtie2 to incorrectly calculate the MAPQ
  when `--mp` was specified in combination with `--ignore-quals`.

v2.4.0-beta2

New changes:

• Fixed an issue in BAM pattern source where one thread would prematurely close the read file pointer
  resulting in other threads crashing because of "Bad file descriptor" errors.

Changes from first beta

• Fixed an issue that would causes bowtie2 to crash with --no-1mm-upfront specified
• Modified bowtie2-build script to better handle of flags and positional parameters
• Migrated all python scripts to python3
• Added support for wildcards input files tobowtie2 wrapper script e.g.
  bowtie2 -x index -q *.fq as opposed to bowtie2 -x index -q 1.fq,2.fq,3.fq...
• Fixed an issue causing bowtie2 to incorrectly process read names see #265
• Added support for allowing presets to be overridden by more specific options e.g
  bowtie2 -x index --local --very-fast-local --L22 -q reads.fq will cause bowtie2 to use a seed length
  or 22 instead of a seed length of 25 that's configured for --very-fast-local preset.
• Modified SAM output for -k/-a so that supplementary alignments get assigned a MAPQ of 255
• Fixed an issue that somtimes causes bowtie2-build to not generate reverse index files
• Added preliminary support for ppc64le architectures with the help of SIMDE project see #271 for details.

v2.4.0-beta

Here are the changes included in this beta.

• Fixed an issue that would causes bowtie2 to crash with --no-1mm-upfront specified
• Modified bowtie2-build script to better handle of flags and positional parameters
• Migrated all python scripts to python3
• Added support for wildcards input files tobowtie2 wrapper script e.g.
  bowtie2 -x index -q *.fq as opposed to bowtie2 -x index -q 1.fq,2.fq,3.fq...
• Fixed an issue causing bowtie2 to incorrectly process read names see #265
• Added support for allowing presets to be overridden by more specific options e.g
  bowtie2 -x index --local --very-fast-local --L22 -q reads.fq will cause bowtie2 to use a seed length
  or 22 instead of a seed length of 25 that's configured for --very-fast-local preset.
• Modified SAM output for -k/-a so that supplementary alignments get assigned a MAPQ of 255
• Fixed an issue that somtimes causes bowtie2-build to not generate reverse index files
• Added preliminary support for ppc64le architectures with the help of SIMDE project see #271 for details.

v2.3.5.1

* Added official support for BAM input files
* Added official support for CMake build system
* Added changes to Makefile for creating Reproducible builds (via [210](https://github.com/BenLangmead/bowtie2/pull/210))
* Fix an issue whereby building on aarch64 would require patching sed commands (via [#243](https://github.com/BenLangmead/bowtie2/pull/243))
* Fix an issue whereby `bowtie2` would incorrectly throw an error while processing `--interleaved` input

v2.3.5

* Added support for obtaining input reads directly from the Sequence Read Archive, via NCBI's [NGS language bindings](https://github.com/ncbi/ngs).  This is activated via the [`--sra-acc`](manual.shtml#bowtie2-options-sra-acc) option.  This implementation is based on Daehwan Kim's in [HISAT2](https://ccb.jhu.edu/software/hisat2).  Supports both unpaired and paired-end inputs.
* Bowtie 2 now compiles on ARM architectures (via [#216](https://github.com/BenLangmead/bowtie2/pull/216))
* `--interleaved` can now be combined with FASTA inputs (worked only with FASTQ before)
* Fixed issue whereby large indexes were not successfully found in the `$BOWTIE2_INDEXES` directory
* Fixed input from FIFOs (e.g. via process substitution) to distinguish gzip-compressed versus uncompressed input
* Fixed issue whereby arguments containing `bz2` `lz4` were misinterpretted as files
* Fixed several compiler warnings
* Fixed issue whereby both ends of a paired-end read could have negative TLEN if they exactly coincided
* Fixed issue whereby `bowtie2-build` would hang on end-of-file (via [#228](https://github.com/BenLangmead/bowtie2/pull/228))
* Fixed issue whereby wrapper script would sometimes create zombie processes (via [#51](https://github.com/BenLangmead/bowtie2/pull/51))
* Fixed issue whereby `bowtie2-build` and `bowtie2-inspect` wrappers would fail on some versions of Python/PyPy
* Replaced old, unhelpful `README.md` in the project with a version that includes badges, links and some highlights from the manual
* Note: BAM input support and CMake build support both remain experimental, but we expect to finalize them in the next release

v2.3.4.3

* Fixed an issue causing `bowtie2-build` and `bowtie2-inspect`
  to output incomplete help text.
* Fixed an issue causing `bowtie2-inspect` to crash.
* Fixed an issue preventing `bowtie2` from processing paired and/or
  unpaired FASTQ reads together with interleaved FASTQ reads.

v2.3.4.2

* Fixed issue causing `bowtie2` to fail in `--fast-local` mode.
* Fixed issue causing `--soft-clipped-unmapped-tlen` to be a positional argument.
* New option `--trim-to N` causes `bowtie2` to trim reads longer
  than `N` bases to exactly `N` bases.  Can trim from either 3'
  or 5' end, e.g. `--trim-to 5:30` trims reads to 30 bases,
  truncating at the 5' end.
* Updated "Building from source" manual section with additional
  instructions on installing TBB.
* Several other updates to manual, including new mentions of
  [Bioconda](http://bioconda.github.io) and
  [Biocontainers](https://biocontainers.pro).
* Fixed an issue preventing `bowtie2` from processing more than
  one pattern source when running single threaded.
* Fixed an issue causing `bowtie2` and `bowtie2-inspect` to crash if
  the index contains a gap-only segment.
* Added experimental BAM input mode `-b`. Works only with unpaired
  input reads and BAM files that are sorted by read name (`samtools
  sort -n`). BAM input mode also supports the following options:
    o `--preserve-sam-tags`: Preserve any optional fields present in BAM record
    o `--align-paired-reads`: Paired-end mode for BAM files
* Added experimental cmake support

v2.3.4.2-alpha.2

• Fixes an issue causing bowtie 2 to crash when aligning reads using the --fast-local mode
• Address feature request: trim reads exceeding a given length

v2.3.4.1

* Fixed an issue with `--reorder` that caused bowtie2 to crash while reordering SAM output

v2.3.4

• Fixed major issue causing corrupt SAM output when using many threads (-p/--threads) on certain systems.
• Fixed an issue whereby bowtie2 processes could overwrite each others' named pipes on HPC systems.
• Fixed an issue causing bowtie2-build and bowtie2-inspect to return prematurely on Windows.
• Fixed issues raised by compiler "sanitizers" that could potentially have caused memory corruption or undefined behavior.
• Added the "continuous FASTA" input format (-F) for aligning all the k-mers in the sequences of a FASTA file. Useful for determining mapability of regions of the genome, and similar tasks.