SeqAn Changelog

What's new in SeqAn 2.0.1

• 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