v1.3.1

* Fixed an overflow issue in `bowtie-build` that would sometimes
  yield corrupt "large" (64-bit) indexes; the resulting index
  would sometimes cause `bowtie` to hang. Note: `bowtie2-build`
  does not have this issue.
* Fixed an issue in `bowtie` causing XM:i SAM optional field to
  sometimes be off by 1 when using the `-m/-M` flags.
* Fixed an issue that would sometimes cause deadlocks in `bowtie`
  when running multithreaded.
* Fixed an issue causing build errors when compiling against
  a pre-C++11 standard.

v1.3.0

• Fixed an issue causing bowtie to report incorrect results when using a Bowtie 2 index.
• New, more efficient implementation of --reorder for keeping SAM output lines in same order as input reads
• Added -x parameter for specifying index. bowtie still supports specifying an index via positional parameter, but this behavior will be deprecated.
• Migrated python scripts to python3.
• Fully removed colorspace functionality.
• Added support for compiling on ARM architectures.
• Fixed an issue preventing bowtie from outputting newlines in --max and --un output files.
• Fixed an issue causing alignment results to vary based on read names.
• Fixed an issue preventing --no-unal from suppressing unmapped reads.
• Removed dependence on some third-party libraries, simplifying the code and improving portability.
• Fix an issue preventing bowtie from running with many threads on big-endian machines.

v1.2.3

* Added support for reading and inspecting Bowtie 2 indexes.
  Bowtie 2 indexes can now be used with either Bowtie or Bowtie 2.
* Added support for building an index from a gzipped-compressed
  FASTA.
* Fixed issue preventing bowtie from reporting repeated alignments
  when -M is specified.
* Fixed issue with -F mode omitting final base of each read.
* Fixed clipping of first letter of first read in batches after first.
* Fixed an issue preventing bowtie wrapper script from finding indexes.

v1.2.2

Update (12/12/2017): We have had to re-release this version of bowtie to address an issue when compiling with pthreads (make NO_TBB=1).

• Fixed major issue causing corrupt SAM output when using many threads (-p/--threads) on certain systems
• Fixed major issue with incorrect alignment offsets being reported in --large-index mode
• Fixed major issue with reads files being skipped when multiple inputs were specified together with -p/--threads
• The official LICENSE of Bowtie was changed to Artistic License 2.0. This fixes an issue with the previous LICENSE, which mistakenly combined elements of different open-source licenses.
• Fixed issue where bowtie would still run for a long time even when -u was set to a small number.
• Fixed spurious "Reads file contained a pattern with more than 1024 quality values" error for some colorspace inputs.
• Fixed issue with --strata sometimes failing to suppress alignments at lower strata.
• Fixed issue with ends of paired-end reads sometimes appearing in non-adjacent lines of the SAM output with -p/--threads >1
• Fixed issue whereby the read name of end #2 was not always truncated at the first whitespace character
• Code simplifications

v1.2.2-beta

Add constructor for initializing batch objects

v1.2.1.1

• Fixed an issue causing Bowtie to segfault when processing reads from stdin

v1.2.1

Please note that Bowtie will be switching to the Artistic 2.0 license in the next release.
Pre-build binaries now include statically linked TBB and zlib libraries no longer requiring
these libraries to be pre-installed

• Fixed an issue which caused Bowtie to hang during parallell index building when running an optimized binary
• Deprecated --refout option. It will be fully removed in the next release
• Added parallel index building with the bowtie2-build --threads option (credit to Aidan Reilly - https://github.com/aidanreilly8)
• Added native support for gzipped read files. The wrapper script is no longer responsible for this, which simplifies the wrapper and improves speed and thread scaling.
• Added support for interleaved paired-end FASTQ inputs (--interleaved)
• Fixed issue where first character of some read names was omitted from SAM output when using tabbed input formats
• Fixed issue that caused Bowtie to hang when aligning FASTA inputs with more than one thread
• Bowtie wrapper now works even when invoked via a symlink in a different directory from the executables
• Fixed issue preventing reading --tab5 input on stdin
• Added --no-unal option for suppressing unmapped reads in SAM output

v1.2.0

This is a major release with some larger and many smaller changes. These notes emphasize the large changes. See commit history for details

• 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.
• --reads-per-batch command line parameter added to specify the number
  of reads to read from input file at once
• 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 (TODO: insert actual flag here). 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 colorspace parsing when primer base is present
• Fixed bugs related to --skip command line option