[Seqan-dev] ANN: New I/O Code in SeqAn, includes BAM/SAM I/O

["Holtgrewe, Manuel" <manuel.holtgrewe@fu-berlin.de>]

Dear all,

the SeqAn team is happy to announce the availability of our updated I/O code. The code is available in the current SVN version and will be available in the 1.4 release we are planning later this year.

New features and improvements include:

* A new stream layer that allows for reading and writing to C++/C 
  streams as well as streams compressed with gzip or bz2.
* Improvements to our FASTA/FASTQ I/O code in terms of 
  performance and robustness.
* A tokenizing/parsing interface that allows for easily writing 
  your own parsers.
* An interface for reading SAM and BAM files record-wise.

The code is fairly stable but might undergo small changes before the release. We are sure that it is highly useful, nevertheless. Please try it out and report any problems to our mailing list or bug tracker.

More information is available in our Tutorial

  http://trac.mi.fu-berlin.de/seqan/wiki/Tutorial

Specifically, the following new chapters are interesting for the new system:

  http://trac.mi.fu-berlin.de/seqan/wiki/Tutorial/FileIO2
  http://trac.mi.fu-berlin.de/seqan/wiki/Tutorial/ReadingSequenceFiles
  http://trac.mi.fu-berlin.de/seqan/wiki/Tutorial/Parsing
  http://trac.mi.fu-berlin.de/seqan/wiki/Tutorial/SamBamIO

Bests,
Manuel