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Merge pull request #846 from esiragusa/release/2.0.0
Release 2.0.0
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| build | ||
| dox/html | ||
| docs/html | ||
| docs2/html | ||
| manual/build | ||
| sandbox | ||
| !sandbox/CMakeLists.txt | ||
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| language: cpp | ||
| compiler: | ||
| - gcc | ||
| - gcc-4.8 | ||
| - clang | ||
| cache: | ||
| apt: true | ||
| directories: | ||
| - _build | ||
| before_script: | ||
| sudo apt-get install -qq cmake python python-nose zlib1g-dev libbz2-dev libboost-dev python-jinja2 | ||
| - sudo apt-get install -qq cmake python python-nose zlib1g-dev libbz2-dev libboost-dev python-jinja2 python-pip | ||
| - sudo pip install -r manual/requirements.txt | ||
| - sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test; | ||
| sudo apt-get update -qq; | ||
| sudo apt-get install -qq gcc-4.8 g++-4.8; | ||
| if [ "$CC" == "gcc" ]; | ||
| then | ||
| export CXX=g++-4.8 CC=gcc-4.8; | ||
| gcc-4.8 --version; | ||
| fi | ||
| script: | ||
| ./util/travis/linux-cibuild.sh |
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| SeqAn Changelog | ||
| --------------- | ||
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| This file summarizes the changes to the SeqAn library and apps. | ||
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| Release 2.0.0 | ||
| ~~~~~~~~~~~~~ | ||
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| 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. | ||
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| Library Updates | ||
| ^^^^^^^^^^^^^^^ | ||
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| - 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. | ||
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| Infrastructure Updates | ||
| ^^^^^^^^^^^^^^^^^^^^^^ | ||
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| - 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 (http://seqan.readthedocs.org). | ||
| - The ``core`` and ``extras`` subfolders have been removed. | ||
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| New Apps | ||
| ^^^^^^^^ | ||
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| - ANISE and BASIL | ||
| - Methods for the detection and assembly of inserted sequence in High-Throughput Sequencing Data. | ||
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| - BS Tools | ||
| - Bisulfite read mapping and SNP and methylation level calling. | ||
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| - Fiona | ||
| - A parallel and automatic strategy for read error correction. | ||
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| - Gustaf | ||
| - Generic mUlti-SpliT Alignment Finder. | ||
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| - Mason 2 | ||
| - A read simulator. | ||
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| - NGS ROI | ||
| - Region of Interest Analysis for NGS Data. | ||
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| - Samcat | ||
| - Concatenate and convert SAM/BAM files (faster than samtools). | ||
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| - Seqcons 2 | ||
| - Compute consensus from sequences sequences with and without approximate alignment information. | ||
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| - Yara | ||
| - Yet another read aligner (replaces Masai). | ||
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| Release 1.4.2 | ||
| ~~~~~~~~~~~~~ | ||
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| Documentation-only release backward compatible with 1.4.1. | ||
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| Release 1.4.1 | ||
| ~~~~~~~~~~~~~ | ||
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| 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. | ||
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| Highlights | ||
| ^^^^^^^^^^ | ||
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| - 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. | ||
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| Selected Bug Fixes | ||
| ^^^^^^^^^^^^^^^^^^ | ||
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| - ``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. | ||
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| Release 1.4 | ||
| ~~~~~~~~~~~ | ||
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| Highlights | ||
| ^^^^^^^^^^ | ||
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| - 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. | ||
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| New Apps | ||
| ^^^^^^^^ | ||
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| - ALF | ||
| - Alignment free sequence comparison. | ||
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| - Breakpoint Calculator | ||
| - Breakpoint computation for genomic alignments. | ||
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| - Masai | ||
| - Fast index-based read mapper. | ||
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| - RazerS 3 | ||
| - Fast filtration-based, parallel read mapper. | ||
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| - SnpStore | ||
| - SNP and small indel calling. | ||
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| Major App Updates | ||
| ^^^^^^^^^^^^^^^^^ | ||
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| - All applications now use the ArgumentParser and have better CLI help. | ||
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| - Rabema | ||
| - Rewritten from scratch, includes BAM support. | ||
| - Greatly lowered memory requirements. | ||
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| - SeqCons | ||
| - Fixing input bugs, supports SAM I/O now. | ||
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| - Stellar | ||
| - Major update improving running time, including bug fixes, and | ||
| allowing for various alphabet types. | ||
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| - MicroRazerS | ||
| - Adding support for SAM output. | ||
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| Major Library Updates | ||
| ^^^^^^^^^^^^^^^^^^^^^ | ||
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| - 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 | ||
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| Major Library Bug Fixes | ||
| ^^^^^^^^^^^^^^^^^^^^^^^ | ||
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| - 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. | ||
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| Miscellaneous | ||
| ^^^^^^^^^^^^^ | ||
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| - 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. |
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