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SeqAn Changelog

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

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.

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

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.
  • 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.