v2.3.4-alpha

Potential fix for issues #155 and #158

v2.3.3.1

* 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

V2.3.3

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

v2.3.2

• 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

v2.3.0

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.
• 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

Release 2.2.9

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.

Release 2.2.8

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.

Release 2.2.7

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.

V2.2.6 - 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.