NEWS

Bowtie 2 NEWS
=============

Bowtie 2 is available for download from the project website,
http://bowtie-bio.sf.net/bowtie2 and on Github,
https://github.com/BenLangmead/bowtie2/releases.  2.0.0-beta1 is
the first version released to the public and 2.5.4 is the latest
version.  Bowtie 2 is licensed under the GPLv3 license.  See `LICENSE'
file for details.

Reporting Issues
================

Please report any issues to the Bowtie 2 Github page or using the Sourceforge bug tracker:

  * https://github.com/BenLangmead/bowtie2/issues
  * https://sourceforge.net/tracker/?group_id=236897&atid=1101606

Version Release History
=======================

## Version 2.5.4 - May 16, 2024 ##

### bowtie2 ###
   * Added `--sam-opt-config` command line option for toggling SAM Opt flags.
     See MANUAL for details.
   * Fixed an issue causing `bowtie2`'s memory usage to increase over time
     when aligning BAM files.
   * Changed bowtie2 to continue flushing output in the event of a partial write.
   * Changed the behavior of `bowtie2-build` to throw an exception if it is unable
     to write the BWT (.1.bt2, .1.rev.bt2). In prior versions `bowtie2-build`, would silently
     ignore the error which has led some to report the absence of the BWT files in
     a "completed" index build.
   * Reverted the changes made in v2.5.0 that sometimes caused unique concordant alignments to be overcounted.

## Version 2.5.3 - Jan 16, 2024 ##

   * Fixed an issue causing `bowtie2`'s memory usage to increase over time.
   * Fixed an issue causing `bowtie2` to crash when processing empty FASTQ records.
   * Fixed an issue that would cause `bowtie2` to erroneously treat `-f` and `-F` as mutually exclusive.
   * Add optional support for `libsais` to `bowtie2-build` for faster index building.
     N.B. -- small indexes are capped at 2GB when using `libsais` as opposed to 4GB when using the
     default blockwise algorithm. See MANUAL for more details.

## Version 2.5.2 - Oct 13, 2023 ##

### bowtie2 ###
  * Fixed an issue preventing `bowtie2` from utilizing the specified number of CPU cores
  * Fixed an issue causing `bowtie2` to segfault when reading compressed inputs on Windows
  * Fixed an issue causing `bowtie2` to segfault while parsing interleaved reads
  * Overhauled the FASTQ parser with better tolerance for empty lines

## Version 2.5.1 - Feb 17, 2023 ##

### bowtie2 ###
  * Fixed an issue affecting `bowtie2` alignment accuracy.
  * Updated the versions of the NCBI `NGS` and `VDB` libraries used by `bowtie2`.
  * Fixed a segmentation fault that would occur while aligning SRA data.
  * Fixed an issue preventing `--un-mates` from properly saving unaligned mates.

## Version 2.5.0 - Oct 31, 2022 ##

### bowtie2 ###
  * Overall improvements in the use of prefetch instructions. (contribution by Igor Sfiligoi)
  * Made input/output fully asynchronous by using a dedicated thread. (contribution by Igor Sfiligoi)
  * Added support for AVX2 256-bit instructions with can be enabled by
    setting the `SSE_AXV2` environment variable at compile time. (contribution by Igor Sfiligoi)
  * Fixed an issue causing `bowtie2` to crash when processing ZSTD
    files with high compression ratios.
  * Changed the way that unique alignments are counted in summary
    message to better match up with filters on SAM output

## Version 2.4.5 - Jan 15, 2022 ##

### bowtie2 ###

  * Fixed issues with `bowtie2` BAM parser that would cause `bowtie2` to
    crash when processing input that was encoded with tools other than
    samtools e.g. Picard.
  * Fixed an issue causing `bowtie2` to drop certain optional fields when
    when aligning BAM reads with the `--preserve-tags` option.
  * Fixed an issue causing `bowtie2` to produce mangled SAM output when
    specifying `--sam-append-comment` together with the `--passthrough`
    option.
  * Appended `GO:query` to SAM `@HD` entry to indicate that reads are
    grouped by query name, bump SAM version to 1.5 to indicate support
    for this change.

### bowtie2-build ###

  * Implemented thread pool to address performance regressions
    introduced during the switch to C++11 threads.
  * Fixed an issue causing masked-sequence metadata to be omitted
    from index. This issue would subsequently result in sequence
    data, `@SQ`, being left out from alignment SAM header.
  * Included `.tmp` extension to index files currenlty being built.
    The extension is removed only upon successful build. This change
    seeks to address the assumption that `bowtie2-build` ran successfully
    without building the reverse indexes.
  * Fixed an issue causing `bowtie2-build` to sometimes incorrectly
    calculate input size. This issue would result in the wrong index type
    being chosen and only happened with GZip compressed files.

### bowtie2-inspect ###

  * Added a new `-o/--output` option to save the output of
    `bowtie2-inspect` to a file instead of being dumped to standard
    output.


## Version 2.4.4 - May 23, 2021 ##

  * Fixed an issue that would sometimes cause deadlocks in `bowtie2`
      when running multithreaded

## Version 2.4.3 - May 13, 2021 ##

  * Replaced TBB concurrency with C++ threads
  * Added native support for processing Zstd-compressed read files
    to bowtie2
  * Added native support for processing Zstd-compressed
    reference-genome files to bowtie2-build
  * Fixed an issue causing `bowtie2` to report incorrect alignments
    on big-endian machines
  * Fixed an issue causing `bowtie2` to incorrectly process BAM
    files on big-endian machines
  * Fixed an issue causing Bowtie2 to set an incorrect MAPQ when AS and
    XS are the maximum for read length
  * Add support for building on Apple M1 processors

## Version 2.4.2 - Oct 5, 2020 ##

  * Fixed an issue that would cause the `bowtie2` wrapper script to throw
    an error when using wrapper-specific arguments.
  * Added new `--sam-append-comment` flag that appends comment from FASTA/Q
    read to corresponding SAM record.
  * Fixed an issue that would cause qupto, `-u`, to overflow when there
    are >= 2^32 query sequences (PR #312).
  * Fixed an issue that would cause bowtie2-build script to incorrectly
    process reference files.

## Version 2.4.1 - Feb 28, 2020 ##

  * Fixed an issue that would cause the `bowtie2` wrapper script to incorrectly
    process certain arguments.

## Version 2.4.0 - Feb 25, 2020 ##

  * Fixed an issue in `-b <bam>` input mode where one might prematurely close the
    read file pointer causing "Bad file descriptor" in other threads
  * Fixed an issue that could cause `bowtie2` to crash in `--no-1mm-upfront` mode
  * Modified `bowtie2-build` to better handle of flags and positional parameters
  * Migrated all `python` scripts to `python3`
  * Added support for wildcards in input files to `bowtie2`, e.g. `bowtie2 -x
    index -q *.fq` as opposed to `bowtie2 -x index -q 1.fq,2.fq,3.fq...`
  * Fixed an issue causing <code>bowtie2</code> to incorrectly process read names
    with slash mates plus extra characters (see
    [#265](https://github.com/BenLangmead/bowtie2/issues/265))
  * Clarified support for overriding presets with more specific options e.g
    `bowtie2 -x index --local --very-fast-local --L22 -q reads.fq` will set the
    seed length to 22, overriding the 25 set by `--very-fast-local`
  * Modified SAM output for `-k`/`-a` so that supplementary alignments get
    assigned a MAPQ of 255
  * Fixed an issue that would sometimes 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))
  * Fixed an issue causing `bowtie2` to incorrectly calculate the MAPQ when `--mp`
    was specified in combination with `--ignore-quals`

## Version 2.3.5.1 - Apr 16, 2019 ##

  * 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

## Version 2.3.5 - Mar 16, 2019 ##

  * 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

## Version 2.3.4.3 - Sep 17, 2018 ##

  * 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.

## Version 2.3.4.2 - Aug 7, 2018 ##

  * 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

Thread-scaling paper appears - July 19, 2018

  * Our latest work on Bowtie's core thread scaling capabilities
    [just appeared Open Access in the journal Bioinformatics](href="https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty648/5055585)

## Version 2.3.4.1 - Feb 3, 2018 ##

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

## Version 2.3.4 - Dec 29, 2017 ##

  * 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.

## Version 2.3.3.1 - Oct 05, 2017 ##

  * Fixed an issue causing input files to be skipped when running
  multi-threaded alignment
  * Fixed an issue causing the first character of a read name to be
  dropped while parsing reads split across multiple input files

## Version 2.3.3 - Sep 09, 2017 ##

From this release forward prepackaged bowtie2 binaries are now
statically linked to the zlib compression library and, the recommended
threading library, TBB. Users who rely on prepackaged builds are
no longer required to have these packages pre-installed. As a result
of the aforementioned changes legacy packages have been discontinued.

  * bowtie2-build now supports gzip-compressed FASTA inputs
  * New --xeq parameter for bowtie2 disambiguates the 'M' CIGAR
    flag. When specified, matches are indicated with the '=' operation and
    mismatches with 'X'
  * Fixed a possible infinite loop during parallel index building due
    to the compiler optimizing away a loop condition
  * Added --soft-clipped-unmapped-tlen parameter for bowtie2 that
    ignores soft-clipped bases when calculating template length (TLEN)
  * Added support for multi-line sequences in FASTA read inputs
  * Expanded explanation of MD:Z field in manual
  * Fixed a crashing bug when output is redirected to a pipe
  * Fixed ambiguity in the SEED alignment policy that sometimes caused -N parameter to be ignored

## Version 2.3.2 - May 05, 2017 ##

  * Added support for interleaved paired-end FASTQ inputs
    (--interleaved)
  * Now reports MREVERSE SAM flag for unaligned end when only one
    end of a pair aligns
  * Fixed issue where first character of some read names was
    omitted from SAM output when using tabbed input formats
  * Added --sam-no-qname-trunc option, which causes entire read
    name, including spaces, to be written to SAM output.  This
    violates SAM specification, but can be useful in applications
    that immediately postprocess the SAM.
  * Fixed compilation error caused by pointer comparison issue
    in aligner_result.cpp
  * Removed termcap and readline dependencies introduced in v2.3.1
  * Fixed compilation issues caused by gzbuffer function when
    compiling with zlib v1.2.3.5 and earlier. Users compiling against
    these libraries will use the zlib default buffer size of 8Kb
    when decompressing read files.
  * Fixed issue that would cause Bowtie 2 hang when aligning FASTA
    inputs with more than one thread

## Version 2.3.1 - Mar 04, 2017 ##

Please note that as of this release Bowtie 2 now has dependencies on zlib and readline libraries.
Make sure that all dependencies are met before attempting to build from source.

  * Added native support for gzipped read files.  The wrapper
    script is no longer responsible for decompression.  This
    simplifies the wrapper and improves speed and thread scalability
    for gzipped inputs.
  * Fixed a bug that caused `bowtie2-build` to crash when the
    first FASTA sequence contains all Ns.
  * Add support for interleaved FASTQ format (`--interleaved`)
  * Empty FASTQ inputs would yield an error in Bowtie 2 2.3.0,
    whereas previous versions would simply align 0 reads and report
    the SAM header as usual.  This version returns to the pre-2.3.0
    behavior, resolving a compatibility issue between TopHat2 and
    Bowtie 2 2.3.0.
  * Fixed a bug whereby combining `--un-conc*` with `-k` or `-a`
    would cause `bowtie2` to print duplicate reads in one or both
    of the `--un-conc*` output files, causing the ends to be
    misaligned.
  * The default `--score-min` for `--local` mode is now `G,20,8`.
    That was the stated default in the documentation for a while,
    but the actual default was `G,0,10` for many versions.  Now the
    default matches the documentation and, we find, yields more
    accurate alignments than `G,0,10`

## Version 2.3.0 - Dec 13, 2016 ##

  * Code related to read parsing was completely rewritten to improve
    scalability to many threads.  In short, the critical section is
    simpler and parses input reads in batches rather than one at a time.
    The improvement applies to all read formats.
  * TBB is now the default threading library.  We consistently found TBB to give
    superior thread scaling.  It is widely available and widely installed.
    That said, we are also preserving a "legacy" version of Bowtie that,
    like previous releases, does not use TBB.  To compile Bowtie source
    in legacy mode use `NO_TBB=1`.  To
    use legacy binaries, download the appropriate binary archive with
    "legacy" in the name.
  * Bowtie now uses a queue-based lock rather
    than a spin or heavyweight lock.  We find this gives superior thread
    scaling; we saw an order-of-magnitude throughput improvements at
    120 threads in one experiment, for example.
  * Unnecessary thread synchronization removed
  * Fixed issue with parsing FASTA records with greater-than symbol in the name
  * Now detects and reports inconsistencies between `--score-min` and `--ma`
  * Changed default for `--bmaxdivn` to yield better memory footprint and running time when building an index with many threads

## Version 2.2.9 - Apr 22, 2016 ##

  * Fixed the multiple threads issue for the bowtie2-build.
  * Fixed a TBB related build issue impacting TBB v4.4.

## Version 2.2.8 - Mar 10, 2016 ##

  * Various website updates.
  * Fixed the bowtie2-build issue that made TBB compilation fail.
  * Fixed the static build for Win32 platform.


## Version 2.2.7 - Feb 10, 2016 ##

  * Added a parallel index build option: bowtie2-build --threads <# threads>.
  * Fixed an issue whereby IUPAC codes (other than A/C/G/T/N) in reads were
    converted to As. Now all non-A/C/G/T characters in reads become Ns.
  * Fixed some compilation issues, including for the Intel C++ Compiler.
  * Removed debugging code that could impede performance for many alignment
    threads.
  * Fixed a few typos in documentation.

## Version 2.2.6 - Jul 22, 2015 ##

  * Switched to a stable sort to avoid some potential reproducibility confusions.
  * Added 'install' target for *nix platforms.
  * Added the Intel TBB option which provides in most situations a better performance
    output. TBB is not present by default in the current build but can be added
    by compiling the source code with WITH_TBB=1 option.
  * Fixed a bug that caused seed lenght to be dependent of the -L and -N parameters order.
  * Fixed a bug that caused --local followed by -N to reset seed lenght to 22 which is
    actually the default value for global.
  * Enable compilation on FreeBSD and clang, although gmake port is still required.
  * Fixed an issue that made bowtie2 compilation process to fail on Snow Leopard.


## Version 2.2.5 - Mar 9, 2015 ##

  * Fixed some situations where incorrectly we could detect a Mavericks platform.
  * Fixed some manual issues including some HTML bad formating.
  * Make sure the wrapper correctly identifies the platform under OSX.
  * Fixed --rg/--rg-id options where included spaces were incorrectly treated.
  * Various documentation fixes added by contributors.
  * Fixed the incorrect behavior where parameter file names may contain spaces.
  * Fixed bugs related with the presence of spaces in the path where bowtie binaries are stored.
  * Improved exception handling for missformated quality values.
  * Improved redundancy checks by correctly account for soft clipping.

## Version 2.2.4 - Oct 22, 2014 ##

  * Fixed a Mavericks OSX specific bug caused by some linkage ambiguities.
  * Added lz4 compression option for the wrapper.
  * Fixed the vanishing --no-unal help line.
  * Added the static linkage for MinGW builds.
  * Added extra seed-hit output.
  * Fixed missing 0-length read in fastq --passthrough output.
  * Fixed an issue that would cause different output in -a mode depending on random seed.

## Version 2.2.3 - May 30, 2014 ##

  * Fixed a bug that made loading an index into memory crash sometimes.
  * Fixed a silent failure to warn the user in case the -x option is missing.
  * Updated al, un, al-conc and un-conc options to avoid confusion in cases
    where the user does not provide a base file name.
  * Fixed a spurious assert that made bowtie2-inspect debug fail.

## Version 2.2.2 - April 10, 2014 ##

  * Improved performance for cases where the reference contains ambiguous
    or masked nucleobases represented by Ns.

## Version 2.2.1 - February 28, 2014 ##

  * Improved way in which index files are loaded for alignment.  Should fix
    efficiency problems on some filesystems.
  * Fixed a bug that made older systems unable to correctly deal with bowtie
    relative symbolic links.
  * Fixed a bug that, for very big indexes, could determine to determine file
    offsets correctly.
  * Fixed a bug where using --no-unal option incorrectly suppressed
    --un/--un-conc output.
  * Dropped a perl dependency that could cause problems on old systems.
  * Added --no-1mm-upfront option and clarified documentation for parameters
    governing the multiseed heuristic.

## Version 2.2.0 - February 10, 2014 ##

  * Improved index querying efficiency using "population count" instructions
    available since SSE4.2.
  * Added support for large and small indexes, removing 4-billion-nucleotide
    barrier.  Bowtie 2 can now be used with reference genomes of any size.
  * Fixed bug that could cause bowtie2-build to crash when reference length
    is close to 4 billion.
  * Fixed issue in bowtie2-inspect that caused -e mode not to output
    nucleotides properly.
  * Added a CL: string to the @PG SAM header to preserve information about
    the aligner binary and paramteres.
  * No longer releasing 32-bit binaries.  Simplified manual and Makefile
    accordingly.
  * Credits to the Intel(r) enabling team for performance optimizations
    included in this release.  Thank you!
  * Phased out CygWin support.
  * Added the .bat generation for Windows.
  * Fixed some issues with some uncommon chars in fasta files.
  * Fixed wrappers so bowtie can now be used with symlinks.

Bowtie 2 on GitHub - February 4, 2014
  * Bowtie 2 source now lives in a public GitHub repository:
    https://github.com/BenLangmead/bowtie2.

## Version 2.1.0 - February 21, 2013 ##

  * Improved multithreading support so that Bowtie 2 now uses native Windows
    threads when compiled on Windows and uses a faster mutex.  Threading
    performance should improve on all platforms.
  * Improved support for building 64-bit binaries for Windows x64 platforms.
  * Bowtie is using a spinlocking mechanism by default.
  * Test option --nospin is no longer available. However bowtie2 can always
    be recompiled with EXTRA_FLAGS="-DNO_SPINLOCK" in order to drop the
    default spinlock usage.

## Version 2.0.6 - January 27, 2013 ##

  * Fixed issue whereby spurious output would be written in --no-unal mode.
  * Fixed issue whereby multiple input files combined with --reorder would
    cause truncated output and a memory spike.
  * Fixed spinlock datatype for Win64 API (LLP64 data model) which made it
    crash when compiled under Windows 7 x64.
  * Fixed bowtie2 wrapper to handle filename/paths operations in a more
    platform independent manner.
  * Added pthread as a default library option under cygwin, and pthreadGC
    for MinGW.
  * Fixed some minor issues that made MinGW compilation fail.

## Version 2.0.5 - January 4, 2013 ##

  * Fixed an issue that would cause excessive memory allocation when aligning
    to very repetitive genomes.
  * Fixed an issue that would cause a pseudo-randomness-related assert to be
    thrown in debug mode under rare circumstances.
  * When bowtie2-build fails, it will now delete index files created so far so
    that invalid index files don't linger.
  * Tokenizer no longer has limit of 10,000 tokens, which was a problem for
    users trying to index a very large number of FASTA files.
  * Updated manual's discussion of the -I and -X options to mention that
    setting them farther apart makes Bowtie 2 slower.
  * Renamed COPYING to LICENSE and created a README to be GitHub-friendly.

## Version 2.0.4 - December 17, 2012 ##

  * Fixed issue whereby --un, --al, --un-conc and --al-conc options would
    incorrectly suppress SAM output.
  * Fixed minor command-line parsing issue in wrapper script.
  * Fixed issue on Windows where wrapper script would fail to find
    bowtie2-align.exe binary.
  * Updated some of the index-building scripts and documentation.
  * Updated author's contact info in usage message.

## Version 2.0.3 - December 14, 2012 ##

  * Fixed thread safely issues that could cause crashes with a large number of
    threads.  Thanks to John O'Neill for identifying these issues.
  * Fixed some problems with pseudo-random number generation that could cause
    unequal distribution of alignments across equally good candidate loci.
  * The --un, --al, --un-conc, and --al-conc options (and their compressed
    analogs) are all much faster now, making it less likely that they become
    the bottleneck when Bowtie 2 is run with large -p.
  * Fixed issue with innaccurate mapping qualities, XS:i, and YS:i flags when
    --no-mixed and --no-discordant are specified at the same time.
  * Fixed some compiler warnings and errors when using clang++ to compile.
  * Fixed race condition in bowtie2 script when named pipes are used.
  * Added more discussion of whitespace in read names to manual.

## Version 2.0.2 - October 31, 2012 ##

  * Fixes a couple small issues pointed out to me immediately after 2.0.1
    release
  * Mac binaries now built on 10.6 in order to be forward-compatible with more
    Mac OS versions
  * Small changes to source to make it compile with gcc versions up to 4.7
    without warnings

## Version 2.0.1 - October 31, 2012 ##

  * First non-beta release.
  * Fixed an issue that would cause Bowtie 2 to use excessive amounts of
    memory for closely-matching and highly repetitive reads under some
    circumstances.
  * Fixed a bug in --mm mode that would fail to report when an index file
    could not be memory-mapped.
  * Added --non-deterministic option, which better matches how some users
    expect the pseudo-random generator inside Bowtie 2 to work.  Normally, if
    you give the same read (same name, sequence and qualities) and --seed, you
    get the same answer.  --non-deterministic breaks that guarantee.  This can
    be more appropriate for datasets where the input contains many identical
    reads (same name, same sequence, same qualities).
  * Fixed a bug in bowtie2-build would yield corrupt index files when memory
    settings were adjusted in the middle of indexing.
  * Clarified in manual that --un (or --un-*) options print reads exactly as
    they appeared in the input, and that they are not necessarily written in
    the same order as they appeared in the input.
  * Fixed issue whereby wrapper would incorrectly interpret arguments with
    --al as a prefix (e.g. --all) as --al.
  * Added option --omit-sec-seq, which causes Bowtie 2 to set SEQ and QUAL
    fields to "*" for secondary alignments.

## Version 2.0.0-beta7 - July 9, 2012 ##

  * Fixed an issue in how Bowtie 2 aligns longer reads in --local mode.  Some
    alignments were incorrectly curtailed on the left-hand side.
  * Fixed issue --un (or --un-*) would fail to output unaligned reads when
    --no-unal was also specified.
  * Fixed issue whereby --un-* were significantly slowing down Bowtie 2 when
    -p was set greater than 1.
  * Fixed issue that would could cause hangs in -a mode or when -k is set
    high.
  * Fixed issue whereby the SAM FLAGS field could be set incorrectly for
    secondary paired-end alignments with -a or -k > 1.
  * When input reads are unpaired, Bowtie 2 no longer removes the trailing /1
    or /2 from the read name.
  * -M option is now deprecated.  It will be removed in subsequent versions.
    What used to be called -M mode is still the default mode, and -k and -a
    are still there alternatives to the default mode, but adjusting the -M
    setting is deprecated.  Use the -D and -R options to adjust the effort
    expended to find valid alignments.
  * Gaps are now left-aligned in a manner similar to BWA and other tools.
  * Fixed issue whereby wrapper script would not pass on exitlevel correctly,
    sometimes spuriously hiding non-0 exitlevel.
  * Added documentation for YT:Z to manual.
  * Fixed documentation describing how Bowtie 2 searches for an index given an
    index basename.
  * Fixed inconsistent documentation for the default value of the -i parameter

## Version 2.0.0-beta6 - May 7, 2012 ##

  * Bowtie 2 now handles longer reads in a more memory-economical fashion,
    which should prevent many out-of-memory issues for longer reads.
  * Error message now produced when -L is set greater than 32.
  * Added a warning message to warn when bowtie2-align binary is being run
    directly, rather than via the wrapper.  Some functionality is provided by
    the wrapper, so Bowtie 2 should always be run via the bowtie2 executable
    rather than bowtie2-align.
  * Fixed an occasional crashing bug that was usually caused by setting the
    seed length relatively short.
  * Fixed an issue whereby the FLAG, RNEXT and PNEXT fields were incorrect for
    some paired-end alignments.  Specifically, this affected paired-end
    alignments where both mates aligned and one or both mates aligned
    non-uniquely.
  * Fixed issue whereby compressed input would sometimes be mishandled.
  * Renamed --sam-* options to omit the "sam-" prefix for brevity.  The old
    option names will also work.
  * Added --no-unal option to suppress SAM records corresponding to unaligned
    reads, i.e., records where FLAG field has 0x4 set.
  * Added --rg-id option and enhanced the documentation for both --rg-id and
    --rg.  Users were confused by the need to specify --rg "ID:(something)" in
    order for the @RG line to be printed; hopefully this is clearer now.
  * Index updates: indexes linked to in the right-hand sidebar have been
    updated to include the unplaced contigs appearing in the UCSC "random"
    FASTA files.  This makes the indexes more complete.  Also, an index for
    the latest mouse assembly, mm10 (AKA "GRCm38") has been added.

## Version 2.0.0-beta5 - December 14, 2011 ##

  * Added --un, --al, --un-conc, and --al-conc options that write unpaired
    and/or paired-end reads to files depending on whether they align at least
    once or fail to align.
  * Added --reorder option.  When enabled, the order of the SAM records output
    by Bowtie 2 will match the order of the input reads even when -p is set
    greater than 1.  This is disabled by default; enabling it makes Bowtie 2
    somewhat slower and use somewhat more memory when -p is set greater than
    1.
  * Changed the default --score-min in --local mode to G,20,8.  This ought to
    improve sensitivity and accuracy in many cases.
  * Improved error reporting.
  * Fixed some minor documentation issues.
  * Note: I am aware of an issue whereby longer reads (>10,000 bp) drive the
    memory footprint way up and often cause an out-of-memory exception.  This
    will be fixed in a future version.

## Version 2.0.0-beta4 - December 5, 2011 ##

  * Accuracy improvements.
  * Speed improvements in some situations.
  * Fixed a handful of crashing bugs.
  * Fixed some documentation bugs.
  * Fixed bug whereby --version worked incorrectly.
  * Fixed formatting bug with MD:Z optional field that would sometimes fail to
    follow a mismatch with a number.
  * Added -D option for controlling the maximum number of seed extensions that
    can fail in a row before we move on.  This option or something like it
    will eventually replace the argument to -M.
  * Added -R option to control maximum number of times re-seeding is attempted
    for a read with repetitive seeds.
  * Changed default to --no-dovetail.  Specifying --dovetail turns it back on.
  * Added second argument for --mp option so that user can set maximum and
    minimum mismatch penalties at once.  Also tweaked the formula for
    calculating the quality-aware mismatch penalty.

## Version 2.0.0-beta3 - November 1, 2011 ##

  * Accuracy improvements.
  * Speed improvements in some situations.
  * Fixed a handful of crashing bugs.
  * Fixed a bug whereby number of repetitively aligned reads could be
    misreported in the summary output.

## Version 2.0.0-beta2 - October 16, 2011 ##

  * Added manual, both included in the download package and on the website.
    The website will always have the manual for the latest version.
  * Added Linux 32-bit and 64-bit binary packages.  Mac OS X packages to come.
    Still working on a Windows package.
  * Fixed a bug that led to crashes when seed-alignment result memory was
    exhausted.
  * Changed the --end-to-end mode --score-min default to be less permissive.
    The previous threshold seemed to be having an adverse effect on accuracy,
    though the fix implemented in this version comes at the expense of some
    sensitivity.
  * Changed the --end-to-end mode -M default to be lower by 2 notches.  This
    offsets any detrimental effect that the previous change would have had on
    speed, without a large adverse impact on accuracy.  As always, setting -M
    higher will yield still greater accuracy at the expense of speed.

## Version 2.0.0-beta1 - September 22, 2011 ##

  * First public release.
  * Caveats: as of now, the manual is incomplete, there's no tutorial, and no
    example genome or example reads.  All these will be fixed in upcoming
    releases.
  * Only a source package is currently available.  Platform-specific binaries
    will be included in future releases.