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Old 07-29-2011, 04:29 AM   #1
holtgrewe
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Location: FU Berlin

Join Date: Jan 2011
Posts: 5
Exclamation ANN: New I/O Code in SeqAn (includes BAM/SAM I/O)

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.

Background: SeqAn is an open source (BSD 3-clause) C++ library of efficient algorithms and data structures for biological sequence analysis. The library applies a unique generic design based on C++ templates that guarantees high performance, generality, extensibility, and integration with other libraries. SeqAn is simplifies the development of new software tools with a minimal loss of performance.

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.

We welcome suggestions for additional feature, and improvements in both code and documentation as well as bug reports through our Trac ticket system and our mailing list.

More information is available in our Tutorial

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

Also, in case you are interested in SeqAn, and have missed our announcement, we will hold a free workshop in Berlin from September 12 to 14. You can find more information here:

Bests,
Manuel
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Old 09-25-2011, 08:28 PM   #2
srividya
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Location: CHENNAI

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Posts: 6
Default SeqAn 1.4 download

Hello,

I am trying to download the SeqAn 1.4 version from trac. But I am unable to do so. Can you please tell me from where I can download them directly. Thanks!

Srividya
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Old 09-26-2011, 12:14 AM   #3
holtgrewe
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Default

Dear Srividya,

there currently is no verison 1.4 Release yet. The following article explains how to get the current development/trunk version using Subversion.

http://trac.mi.fu-berlin.de/seqan/wi...GettingStarted

HTH,
Manuel
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