# SeqAn Changelog

This file summarizes the changes to the SeqAn library and apps.

## Release 2.5.3

### Platform Support

* Support for new compilers: Clang 22.
* Compiler support (tested):
  * GCC 13, 14, 15
  * Clang 20, 21, 22
  * Intel oneAPI C++ Compiler 2025.0 (IntelLLVM)
  * Microsoft Visual Studio 17
  * Other compilers might work but are not tested.

### Selected Bug Fixes

* I/O:
  * Fixed discarded `nodiscard` values for Clang 22.
  * Resolved a rare data race in the BGZF stream.
* Yara:
  * Incorporated safeguards to prevent out of bounds access in certain edge cases.

## Release 2.5.2

### Platform Support

* Support for new compilers: Clang 21.
* Compiler support (tested):
  * GCC 13, 14, 15
  * Clang 19, 20, 21
  * Intel oneAPI C++ Compiler 2025.0 (IntelLLVM)
  * Microsoft Visual Studio 17
  * Other compilers might work but are not tested.

### Selected Bug Fixes

* Build System:
  * Fixed CMake install relative path and CTD generation.
* Argument Parser:
  * Added support for unsigned 64-bit integers.
* Mason:
  * Fixed VCF output not using format properly.
  * Fixed acceptance of 64-bit seeds.
  * Improved parallel output performance by writing directly without temporary files.
* Compiler Compatibility:
  * Fixed internal compiler error on MSVC 19.44.
  * Fixed deprecated `#pragma omp master` for GCC 16.
  * Fixed various warnings and issues for GCC 16 compatibility.

## Release 2.5.1

### Platform Support

* Support for new compilers: GCC 15 and Clang 20.
* Compiler support (tested):
  * GCC 13, 14, 15
  * Clang 18, 19, 20
  * Intel oneAPI C++ Compiler 2025.0 (IntelLLVM)
  * Microsoft Visual Studio 17
  * Other compilers might work but are not tested.

### Selected Bug Fixes

* Build System:
  * Fixed an issue in our CMake files that resulted in `SEQAN_DEFINITIONS` being incorrectly set.
    With this fix, using `target_link_libraries (my_target seqan::seqan2)` instead of setting various variables
    individually now works as expected.
    ```diff
    - include_directories (${SEQAN_INCLUDE_DIRS})
    - add_definitions (${SEQAN_DEFINITIONS})
    - set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${SEQAN_CXX_FLAGS}")
    - target_link_libraries (my_project ${SEQAN_LIBRARIES})
    + target_link_libraries (my_project seqan::seqan2)
    ```
* Mason:
  * An exception will be thrown when Mason runs out of temporary disk space instead of crashing.
    The exception message contains instructions to resolve the issue by setting the `TMPDIR` environment variable,
    which are also available in the *Caveats* section of the help page.

## Release 2.5.0

This release adds support for newer compilers and C++ standards (17, 20, 23).
It also improves interoperability with [SeqAn3](https://github.com/seqan/seqan3).

### Namespace

To avoid namespace conflicts with other libraries in the SeqAn ecosystem, the namespace was changed
from `seqan` to `seqan2`.

To use version 2.5.0, you will need to update your code.
Depending on how you use seqan in your project, the following changes are required:

```cpp
// Before
using namespace seqan;
// After
using namespace seqan2;
```

```cpp
// Before
auto foo(seqan::StringSet<seqan::DnaString> const & sequences)
{
    return seqan::length(sequences);
}
// After
auto foo(seqan2::StringSet<seqan2::DnaString> const & sequences)
{
    return seqan2::length(sequences);
}
```

A script to automatically update your code may look like this:
```bash
for file in $(git grep -l 'namespace seqan'); do sed -i 's/namespace seqan/namespace seqan2/g' ${file}; done
for file in $(git grep -l 'seqan::'); do sed -i 's/seqan::/seqan2::/g' ${file}; done
```

### Library Features

* Sequence I/O:
  * Accepting files that end in `.fas`.
* Indexing:
  * Improved search schemes for 3 and 4 errors in `seqan2::bi_fm_index`.

### Selected Bug Fixes

* VCF I/O:
  * Accessing the const reference of a `seqan2::VcfIOContext` via `seqan2::context` now works correctly.
* Indexing:
  * horspool: If the text is smaller than the query, abort the search.
* BAM I/O:
  * The output now includes the SQ header lines.

### App Updates

* Yara:
  * Fixed verification of N's for seeds and boundary checking for anchors (restores full-sensitivity)
  * Removed option --all (was deprecated)
  * Added option to compute and output alignments for secondary matches
  * Added option to specify strata threshold as absolute number of errors
* Mason:
  * Fixed various bugs that resulted in crashes or incorrect output.
  * The help page now lists common caveats and how to avoid them.
  * simulator: Now uses the command line parameter for seeding instead of the default.
  * **simulator**: Removed simulation of 'N', the output will only contain 'A', 'C', 'G', 'T'.
  * simulator: Alignment output (`--out-alignment`) in conjunction with bisulfite sequencing (`--enable-bs-seq`) now
    yields correct reference begin positions.

### Build System

* The minimum CMake version requirement was raised to 3.12.

### Platform Support

* Compiler support (tested):
  * GCC 12, 13, 14
  * Clang 17, 18, 19
  * Intel oneAPI C++ Compiler 2025.0 (IntelLLVM)
  * Microsoft Visual Studio 17
  * Other compilers might work but are not tested.

## Release 2.4.0

### Library Features

* Align
  * Generic parallelisation and vectorisation.
  * Support for SSE4, AVX2 and AVX512.
  * Speed-Ups of > 1000x compared to serial execution of long DNA alignments.
* Indexing
  * Parallel `find()` interface
  * Support for optimal search schemes (https://arxiv.org/abs/1711.02035)
* ReducedAminoAcid
  * several new Reduced Amino Acid alphabets are now available.
* VCF I/O
  * Now supports version 4.2 of the specification, i.e. columns with only eight fields.

### Selected Bug Fixes

* BAM I/O
  * Fix of jumpToRegion() functionality to start at the desired region instead of the index block.
  * Works correctly on big endian platforms now.
* Translation
  * Handle empty/too-short input correctly.
* Code Cleanup
  * various parts of the codebase have undergone cleanup and may now report deprecated functionality as being deprecated
    via compiler-functionality.

### Platform Support

* Compiler support:
  * Satisfies stricter warning levels of GCC-8, Clang-5 also with `-std=c++17`.
  * Supports VS2017.
  * Intel Compiler suite 2016 **was dropped**.
  * Intel Compiler suites 2017 and 2018 are newly supported.
  * GCC-4.9 on MacOS **was dropped** (newer GCC available everywhere via MacPorts or Homebrew).
  * Clang-3.5 on FreeBSD **was dropped** (newer Clang available in base system and Ports).
* CPU architectures support:
  * Substantial fixes for big endian platforms
  * Now officially supported and passing integration tests:
    * `i386, amd64/intel64, x32, ia64`
    * `armel, armhf, arm64`
    * `mips, mipsel, mips64el`
    * `powerpc, ppc64, ppc64el`
    * `s390x, alpha, m68k, sh4`
  * Officially **not** supported: `sparc64`
  * Thanks to the [Debian Med team](https://www.debian.org/devel/debian-med/) for their patches!
* Upstream packages:
  * SeqAn2 packages are finally coming to Fedora, thanks to @sagitter
  * Package updates in Debian, Ubuntu, MacPorts, Homebrew and FreeBSD expected shortly.

## Release 2.3.2

### Selected Bug Fixes

* Argument parser
  * various fixes in the version checker
  * fix incompatibilities in CTD file creation with KNIME (introduced in 2.3.0)
* Build systems
  * reintroduce `FindSeqAn.cmake` for projects that rely on cmake's module mode
  * fix the pkgconfig file
* Platform related
  * improved compliance with warning levels of soon-to-be-released gcc7 and clang4
  * because of unresolved bugs we now recommend gcc5 as minimum gcc version when using static linking

## Release 2.3.1

### Selected Bug Fixes

* Argument parser
  * bool option negative values
  * improve and fix version check

## Release 2.3.0

### Library Features

* Argument Parser:
  * Adds version check support to the argument parser.
    * Check for new updates of a specific application.
    * Check for new versions of the library.
    * This option is opt-out by default but can be switched to opt-in or completely disabled via compiler flags and the
      SeqAn build system.
  * Altered Argument Parsers help page to display argument information.
  * Extended Argument types by bool, input_directory and output_directory.
  * Display file extensions that contain numbers.
* Sequence I/O:
  * New support for RNA structure files
    * Supported formats: Vienna (.dbv), Dot-Bracket-Notation (.dbn), Stockholm (.sth), Connect (.ct), Bpseq (.bpseq),
      Extended Bpseq (.ebpseq)
    * Input/output of whole files or of a single record/header
  * Added function isOpen() for formatted files.
  * Enabling assignment of format tags that differ from underlying format.
  * It is now possible to treat a BAM file as a (compressed) sequence file and read the sequences as if they were FastQ.
* Blast I/O:
  * Added support for handling the `Q_ACC`, `S_ACC`, `S_ALLACC`, `S_TAX_IDS` fields
  * Added non standard fields `LCA_ID` and `LCA_TAX_ID` for lowest common ancestor information
  * Moved some redundant data from matches into record objects
* FM Index:
  * Added documentation for the bidirectional FM index
  * Reduced size of constant-time FM index
* Graphs:
  * Added new function getVertexAdjacencyVector()

### Selected Bug Fixes

* Sequences:
  * Initialize empty CStyle Strings properly.
  * Fixed length function for const Dependent-StringSet
* Graphs:
  * Reimplemented DFS in a non-recursive fashion to avoid stack overflow.
  * Multiple Sequence Alignment: Fix getAlignmentStatistics() on empty `matches` string.
* Alignments:
  * Banded Chain Alignment: check for possible score overflow.
* GFF / GTF:
  * Fixed I/O compatibility
    * Ignoring additional space
    * Allowing records to have multiple parents
* BAM I/O:
  * Parsing the header for SO tags
* VCF I/O:
  * Fixed reading of contig names in VCF header
* Indices:
  * Enforce Container-Types for find()

### App Updates

* Gustaf:
  * Fixed name conflict (TANDEM)

### Platform Support

* Compiler support:
  * SeqAn satisfies stricter warning levels of GCC7 and c++1z
* New operating systems supported:
  * (Debian) GNU/kFreeBSD and GNU/Hurd
* New CPU architectures supported:
  * `arm` and `arm64`, `mips` and `mips64`
  * `powerpc`, `powerpc64` and `sparc64`
  * and some others (all Debian platforms except `sh4` and `armel`)
* Thanks to the Debian Med team for their patches

### Infrastructure Updates

* Added feature to selectively deactive the build of individual apps
* Enforce using Python 2.x for documentation
* Improvements to CMake and PkgConfig files

## Release 2.2.0

### Library Features

* Indices:
  * FM index now has several options to reduce space consumption or improve running time
    * up to three level rank dictionaries
    * size of blocks on the lowest level (referred to as `WORDS_PER_BLOCK`)
  * Bidirectional FM index with constant running time using EPR-dictionaries
  * Please see the [manual](seqan.readthedocs.io/en/main/Tutorial/DataStructures/Indices/FMIndex.html) for more
    information
* Alignment:
  * Vectorized DP-Alignment algorithms using SSE3/AVX2. Allows for inter-parallel alignment computation in a
    many-vs-many or one-vs-many mode.
  * add a scoring matrix type that can be specified at runtime (e.g. BLOSSUM62, BLOSSUM50)
* Modifier:
  * ModifiedString ModPadding: Expand a string with padding symbols, without changing the source.
* Other:
  * Replace pthread implementation with STLs thread support library. Increases performance and fixes rare bugs in
    bam_io.

### App Updates

* SAK (Swiss Army Knife):
  * fixed sequence filters.
* Yara:
  * verifying seeds
  * fixes CIGARs and secondary records.

### Selected Bug Fixes

* Alignments:
  * fixes MyersHirschberg implementation.
  * accept '=' operations in CIGAR string
* Split Alignment:
  * computes correct trace from split position.
  * allows flexible free-end gaps configuration.
* close Fasta file after FAI-Index is built.
* fixes Character to AminoAcid conversion.
* remove temporary files created during tests on Windows.

### Infrastructure Updates

* Build System:
  * The Intel Compiler is now fully supported on Linux and Windows, both 32bit and 64bit; it builds faster binaries and
    supports some functionality not available in MSVC.
  * On Windows there is now experimental support for Clang/C2, the Microsoft version of the clang compiler.
  * Please see the [manual](https://seqan.readthedocs.io/en/main/Infrastructure/Use/CMakeBuildDirs.html#visual-studio)
    for more information on how to use these compilers.
  * support deb/rpm/exe/dmg packages and SSE4+POPCNT binaries
* Platforms:
  * full FreeBSD support
  * Ship UCRT, OPENMP and Intel DLLs for apps on windows
  * more apps available on Windows and some packaging fixes

### Documentation Updates

* Api Docs:
  * Tree-View by Module

## Release 2.1.1

Minor release including major improvements of the manual, several library bug-fixes and changes in the build system. All
library modules are backward compatible with 2.1.0. For a complete list of changes visit
[GitHub](https://github.com/seqan/seqan/pulls?q=is%3Apr+is%3Amerged++milestone%3A%22Release+2.1.1%22+).

### Selected Bug Fixes

* Tests:
  * delete automatically created temp directories in unit and app tests
  * demo tests: `std::cout` was not considered in tests

### App Updates

* Yara:
  * fall back to single-end mapping when paired-end library length distribution is neither given nor estimable
  * fixed handling of reference metagenomes (references larger than 16k sequences)
  * enabled support for reference metagenomes by default (`-DYARA_LARGE_CONTIGS=ON`)
  * added option `--sensitivity` (low, high, full)
  * replaced option --output-secondary with `--secondary-alignments` (tag, record, omit)
  * renamed several options

### Documentation Updates

* Manual:
  * major reworking of the manual
  * repaired links to API dox
  * hourly update of API dox for nightly builds

### Infrastructure Updates

* Build System:
  * more sensible execinfo detection
  * don't ship apps and the manual on library releases
  * introduce cmake `-DSEQAN_OFFICIAL_PKGS=1` to build upstream releases with static binaries
  * cache dependency detection on `DEVELOP`
  * make it possible to do `RELEASE_LIBRARY` without dox
* Platforms:
  * basic BSD support
  * fixed warnings on Windows
* KNIME:
  * packaging - more flexibility when generating KNIME plugins of external apps

## Release 2.1.0

Major release with many new features and applications. Except where noted below, this release is compatible to previous
2.x releases. For a complete list of changes visit
[GitHub](https://github.com/seqan/seqan/pulls?q=is%3Apr+is%3Amerged++milestone%3A%22Release+2.1.0%22+).

### Library Updates and Selected Bugfixes

* Apps:
  * Yara: fixed warnings, build errors and bugs, updated test files
  * Yara: new features (compute mapping qualities, estimate distribution of paired-end insert sizes)
  * Yara: follow SAM recommended practices for paired-end reads
  * T-Coffee: new feature `deep coffee` (aligning several hundred sequences)
  * Gustaf: introduced two phase breakpoint combination; updated readme and help messages
  * Removed old apps: Razers2, Flexbar and SeqCons in favor of newer releases
* Alignments:
  * added feature to count gaps to the left a of a position/iterator
  * disallow wrong use of scoring scheme for Hirschberg algorithm
  * extended AlignmentStats by number of gaps and length of the alignment
  * fixed evaluation of alignment
  * using gaps for integrateAlign and align_extend
* BLAST (new module):
  * E-Value statistics, including precomputed constants, bit-score and e-value calculation for alignments
  * support for reading and writing BLAST Tabular files (with and without comments)
  * support for writing BLAST Report files
* Indices:
  * added public function for trie and radix tree construction
  * Q-gram Index: allows sorting the hash-table according to the number of occurrences to reduce cache misses
* IO:
  * Tabix index: allowing range queries on chromosomal file formats such as VCF
  * Fai Index: optimized fasta index construction
  * BAM: added function to write tags from BamTagsDict to the tags field of a bam record
  * BAM: allowed BamTagsDict to take const CharStrings
* Misc:
  * fixed Iupac alphabet by replacing `=` by `U`
  * added missing `O` character to amino acid alphabet
  * Argument Parser: a few new features such as help string for advanced options
  * removed random number engine and replaced it by the STL one
  * ZipIterator & ZipContainerView: iterating simultaneously over multiple containers
  * extended edges in graphs to store a reference to its source
* Modifier:
  * ModifiedString ModPos: iterating over a sequence in a predefined order
  * overload save() of ModifiedStrings for const strings
  * fixed Modified Iterators and ModView
* Journaled String Tree (new module):
  * reference compressed string set structure
  * for more details see the [publication](https://bioinformatics.oxfordjournals.org/content/30/24/3499.short)
* STL containers:
  * added a completely new adaptation to SeqAn interfaces that supports all STL containers, also `std::array` and
    `std::forward_list`
  * greatly improved compatibility of SeqAn algorithms with STL containers so these can be used instead of SeqAn Strings
* Streams:
  * improved ZipStream
* Compatibility to previous versions
  * the random module was removed, please use the STL's random module instead
  * the `StringSet<T, Dependent<Tight> >` has been deprecated and will likely be removed for the next release
  * some SeqAn Macros have been deprecated since C++11 is now required, e.g. there is no `SEQAN_AUTO_PTR_NAME`, only
    `unique_ptr<>`
  * `SEQAN_NAMESPACE_MAIN` has been moved into the `seqan` namespace, so some of your Metafunction overrides may need to
    be adapted

### Documentation Updates

* Dox:
  * added version selector in API dox

### Infrastructure Updates

* Build System:
  * Major improvements to build system resulting in cleanup and dropped dependencies
  * C++11 is now required and many datatypes now have move cosntructors and -assignment operators
  * added support for new compiler versions, but dropped support for older compilers
  * requirements are now GCC ≥ 4.9 or LLVM / Clang ≥ 3.5 (for Linux, Mac OSX, FreeBSD) and Visual C++ ≥ 14.0 / Visual
    Studio ≥ 2015 (for Windows)

## Release 2.0.2

Minor release including several library bug-fixes as well as better documentation and infrastructure. All library
modules are backward compatible with 2.0.1. For a complete list of changes visit
[GitHub](https://github.com/seqan/seqan/pulls?q=is%3Apr+is%3Amerged++milestone%3A%22Release+2.0.2%22+).

### Selected Bug Fixes

* Sequences:
  * fixed insert() for packed_string
  * fixed segfault bug for upac assignment in Dna5 StringSet
  * added insertValue(), insert() and replace() for StringSets
  * added empty() for std::list
* IO:
  * BAM I/O: adding spport for custom tags with floats
  * BAM I/O: BamTagsDict allows wrapping a const object
  * FastQ: fixed readRecord() for malformed fastq files (avoid skipping records)
  * FaiIndex: fixed readSequence/readRegion allocation
* Apps:
  * Gustaf: loading Fasta files with Iupac characters

### Documentation Updates

* Dox:
  * fixed page redirection
  * minor bugs
  * code snippets in the documentation now undergo build tests and continuous integration to avoid outdated
    documentation

### Infrastructure Updates

* Platform Support:
  * FreeBSD support
  * updated prerequisites for GCC to >= 4.7 and Clang to >= 3.3
  * fixed warnings for gcc6
  * clang-3.7.x: deactivated openmp because of bug
  * fixed compiler-warnings in Visual Studio (/W2 produces no warnings anymore)
  * added support for Visual Studio 2014 and 2015
* Build System:
  * added pkg-config support
  * changed includes search priorities for CMake's FindSeqAn
* Continuous Integration:
  * added more platforms on TravisCI

## Release 2.0.1

Minor release including several library bug-fixes as well as better documentation and infrastructure. All library
modules are backward compatible with 2.0.0. For a complete list of changes visit
[GitHub](https://github.com/seqan/seqan/pulls?q=is%3Apr+is%3Amerged++milestone%3A%22Release+2.0.1%22+).

### Library Bug Fixes

* Basic:
  * Added AminoAcid symbol "O"
  * Disabled global exception handler by default
* Sequence:
  * Added missing overloads for const Strings
  * Fixed and tested StringSet
  * Reworked STL containers adaption
  * Fixed several bugs in ModifiedStrings and ModifiedIterators
* Stream:
  * Worked around I/O with std::string
  * Supported multi-stream gzip files produced by Illumina Casava
  * Fixed BgzfStream tell()
* SeqIO:
  * Changed Raw file extension from .txt to .raw
* BAM I/O:
  * Fixed BIN computation
  * Fixed a bug in jumpToOrphans()
  * Fixed internal concurrency problems
  * Fixed readBamHeader() to clear the BamHeader
  * Added assertions to writeRecord()
  * Added BamIndex::save() to save .bai files
* Gff I/O:
  * Fixed parsing of comment lines
* FragmentStore:
  * Fixed loading Gtf/Gff3 files
* Index:
  * Fixed open() and save() for WT FMIndex
  * Added open() and save() for OpenAddressing QGramIndex
* Seeds:
  * Fixed a bug in sparse chaining
  * Fixed a bug in banded chain alignment

### Documentation Updates

* Manual:
  * Fixed and improved several Tutorials and HowTos
  * Added version-aware links to the dox
* Dox:
  * Added @datarace entity
  * Fixed broken links in "See Also" section
  * Fixed a problem with close button in the side pane
  * Documented class VirtualStream
* Demos:
  * Restructured demos directory
  * Fixed several broken demos

### Infrastructure Updates

* Platform Support:
  * Added support for GCC 4.9 and Clang 3.7
  * Preliminary support for Clang 3.8 with OpenMP
  * Preliminary support for Visual Studio 2015
  * Preliminary support for FreeBSD 10.2
* Build System:
  * Tested all demos
  * Upgraged TravisCI builds to run on Docker
  * Fixed Java detection

## Release 2.0.0

Major release with many new features and applications. Note, the majority of the modules are backward compatible to the
previous version. Some modules, e.g. I/O-modules, have some adapted easier-to-use or unified interfaces.

### Library Updates

* Faster and easier-to-use modules for basic and formatted file I/O:
  * `stream`
  * `seq_io`
  * `bam_io`
  * `vcf_io`
  * `gff_io`
* Faster data structures:
  * FMIndex (up to 4X).
  * Packed Strings.
* New alignment modules:
  * X-Drop extension for alignments (`align_extend`)
  * Sequence-profile alignments (`align_profile`)
* New AminoAcid-Dna translation module (`translation`)
* The motif finding module (`find_module`) has been removed.

### Infrastructure Updates

* The repository has been migrated to GitHub (https://github.com/seqan/seqan).
* Continuous integration builds happen on TravisCI.
* The manual has been migrated to sphinx (https://seqan.readthedocs.io).
* The `core` and `extras` subfolders have been removed.

### New Apps

* ANISE and BASIL
  * Methods for the detection and assembly of inserted sequence in High-Throughput Sequencing Data.
* BS Tools
  * Bisulfite read mapping and SNP and methylation level calling.
* Fiona
  * A parallel and automatic strategy for read error correction.
* Gustaf
  * Generic mUlti-SpliT Alignment Finder.
* Mason 2
  * A read simulator.
* NGS ROI
  * Region of Interest Analysis for NGS Data.
* Samcat
  * Concatenate and convert SAM/BAM files (faster than samtools).
* Seqcons 2
  * Compute consensus from sequences sequences with and without approximate alignment information.
* Yara
  * Yet another read aligner (replaces Masai).

## Release 1.4.2

Documentation-only release backward compatible with 1.4.1.

## Release 1.4.1

This minor release should be backward compatible with 1.4. It contains small fixes and many demos for improving the API
documentation. Some file format functionality has been added.

### Highlights

* Many new demos and improved API documentation throughout the library.
* New file format support and tutorials for this functionality: VCF I/O, BED I/O, and improvements to GFF and GTF I/O.

### Selected Bug Fixes

* `gff_io.h` does not contain corrupt includes any more
* Gapped X-drop seed extension now works with score matrices such as BLOSUM60.
* SAM writer code now writes `255` for invalid `MAPQ` and `0` for invalid/unapplicable `TLEN` instead of `*`.
* Fix in Postorder ParentLinks VSTree Iterator.
* `SEQAN_PATH_TO_ROOT()` can now be used in demo programs.
* Removing duplicate definition of `SEQAN_ENABLE_TESTING` in build system.
* Write support for `char *` for `BamTagsDict`.
* Fix in `StringEnumerator`.
* Fix writing out of file extension when writing KNIME plugins.

## Release 1.4

### Highlights

* New read mappers applications Masai and RazerS 3.
* Extended and more robust I/O functionality in `stream`, `seq_io`, `bam_io`, and `gff_io`.
* Module arg_parse creates improved command line help and supports workflow engine integration.
  * Also see https://github.com/genericworkflownodes
* Greatly improved alignment module with better performance and interfaces.
* Greatly improved build system, `find_package(SeqAn)` for your CMake build systems.

### New Apps

* ALF
  * Alignment free sequence comparison.
* Breakpoint Calculator
  * Breakpoint computation for genomic alignments.
* Masai
  * Fast index-based read mapper.
* RazerS 3
  * Fast filtration-based, parallel read mapper.
* SnpStore
  * SNP and small indel calling.

### Major App Updates

* All applications now use the ArgumentParser and have better CLI help.
* Rabema
  * Rewritten from scratch, includes BAM support.
  * Greatly lowered memory requirements.
* SeqCons
  * Fixing input bugs, supports SAM I/O now.
* Stellar
  * Major update improving running time, including bug fixes, and allowing for various alphabet types.
* MicroRazerS
  * Adding support for SAM output.

### Major Library Updates

* Modules `seq_io`, `bam_io`, `gff_io` with I/O functionality.
* FM Index in module `index`.
* Rewritten `align` module with better performance, more consistent interfaces.
* Split alignment module `align_split`.
* Metaprogramming: introducing `EnableIf`, `DisableIf`, `EnableIf2`, and `DisableIf2` metafunctions
* Module `alignment_free` for alignment free sequence comparison.
* Module `journaled_set` for managing many similar sequences.
* Faster open addressing q-gram index.
* generic support for memory mapped files via FileMapping class
* Adding module `parallel` with atomic operations in C++98.
* Greatly improved FragmentStore documentation.
* Adding `position()`, `operator-()`, `operator[]` with proxy functionality and relation operators to journaled string
  iterator.
* Pigeonhole-based filter algorithm.
* Parallel repeat finding.
* Clang support, C++11 support

### Major Library Bug Fixes

* Fixing repeat finding on Dna5Q.
* Fixing insert size computation in store_all.h
* Fixing memory initialization problem in `appendValue()` for Block String.
* Default constructor of Iter modified, such that data_container and data_position are initialized.
* Fixed error loading Fasta on Windows.
* Fixed wrong StringSet size types, allow to easily subclass Alloc strings
* Now supports SAM files with missing read sequences
* Fixing SeqAn code for C++11
* FragmentStore fixes.

### Miscellaneous

* Experimental support added platforms for ICC and PGI compilers.
* Experimental support for CUDA.
* Build System
  * Large updates to build system.
  * Includes `FindSeqAn.cmake` for easily using SeqAn in your own CMake build system.
  * Packaging now based on CPack
* Xcode plugin for MacPorts LLVM/Clang in Xcode 3 and 4
* Improved code generator `skel.py`.
* Many minor bug fixes
* Cleaned code base
* Added test cases (e.g. Stellar)
* Improved documentation and added examples (Mason, Rabema, RazerS, etc.)
* Improving coding style compliance of Array String implementation.
* Various tool improvements (e.g. RazerS 3)
* Performance improvements.
