wiki:Retreat2010/NewFeatures
Last modified 17 months ago

New Features

After Release 1.3, we will collect all changes in a CHANGELOG file in the repository with each commit that contains the changes. However, before that we will collect a list here.

Headlines:

  • Functionality
    • New full sensitivity local aligner stellar (Blast speed for genome sized data)
    • New split read mapper splazers
    • New journaled string data structure
    • New random function generator
    • Completely refurbished score module.
    • New fragment store for 2nd generation sequencing:
      • Represents multi-read alignments and genome annotations
      • Supports SAM, Amos, GFF, GTF, UCSC Genome Browser formats
      • Can be displayed as a visual SVG file
    • New read simulator mason
  • Development support
    • New test system. Templates for applications and tests are available.
    • Harmonized naming conventions.
  • Documentation and Distribution
    • Added a new WIKI based tutorial
    • The documentation can now be built in less than one minute.
  • Changed license to 3-clause BSD license.
  • Nightly documentation builds can be found at www.seqan.de/dddoc/html_devel/
  • Current changes in the trunk can now be found in the file projects/library/CHANGELOG and on the wiki at ChangeLog.

Changelog

  • Various identifier have been renamed (list of renamed identifiers).
  • SeqAn is now built nightly and errors are reported to our  CDash Dashboard.
  • We dropped Support for Visual Studio 7, GCC 3.x and added support for LLVM and more current Visual Studio and GCC versions. The full list now is:
    • On Windows: Visual Studio 8, Visual Studio 9, and Visual Studio 10, MinGW
    • On Mac Os X and Linux: GCC 4.1-4.5 as well as the current LLVM trunk version.
  • Experimental seeds2 module replacing module seeds in the future.
  • Overhauled test system.
  • Documentation building is much faster now.
  • Added journaled string feature in module string_journaled.
  • Added swiss army knife (sak) tool for slicing and dicing DNA files (FASTA, FASTQ).
  • Added RNA alphabet
  • Implemented local version of the SWIFT filter additionally to semi-global version (index/find_swift.h).
  • Added banded local alignment
  • Fixed assignments between infixes and suffixes (#320).
  • Patterns provide a copy constructor now (#318).
  • Fixed StringSet documentation: Default specialization (#275).
  • Fixed problem in suffix array implementation with max repeat calculation (#61).
  • Fixed _MakeSigned metafunction to work with unsigned long long.
  • Changing Infix Segment constructor to construct an infix of the whole string if no begin and end positions are given (#288).
  • Listing headers to include for each symbol in the documentation (#25).
  • Added much more documentation, fixing some issues (#326, #330).
  • Documentation works now correctly in Opera.
  • Fixed bug of insertValue with String of CharStrings (#273).
  • ModifiedStrings can now be appended to std::string objects (#251).
  • Implementing std::swap for StringSet and String (#296).
  • Fixing bug in assignSource and globalAlignment.
  • Fixing issue with missing needle in MyersUkkonen (#319).
  • Indices can be built in StringSets of Segments now (#191).
  • HMM algorithms use the new random module now (#351).
  • Fixing collision with begin and end in C++0x (#374).
  • operator- is now implemented for iterators of a string and infixes of a string (#317).
  • Unused reference counting feature of Holder is removed (#381).
  • Documented haystack, host, needle more clearly (#371).
  • atEnd() now works for StringSet iterators (#84).
  • The command line parser now accepts floating point arguments (#295).
  • Pdf<Uniform> now works correctly with float types (#502).
  • Line endings are set to native now via the svn:eol-style property (#386).
  • Non-external nested typedefs are suffixed with an underscore now to prevent accidental access (#289).
  • Naming of acronyms is more consistent now (#73).
  • Internal symbols for tag definitions do not violate the C++ standard any more (#290).
  • fill has been renamed to resize (#77).
  • added std::vector adaptions (#381)

Deprecations

  • supremumValue, infimumValue are deprecated
  • The find_motif module has known issues and will be replaced in a future version.
  • The seeds module has known issues. There is an experimental new version seeds2 available in SeqAn trunk that will eventually replace seeds in the next release.
  • Currently, all non-container values (e.g. int, char*, even custom structs) are interpreted to be containers of length 1. This feature is rarely, if ever, used and will not be available in future releases.