Re: [Seqan-dev] SeqAn-v2.0.0

[Rahn, René <rene.maerker@fu-berlin.de>]

Hey Fedor, 

thanks for reporting this. 

We updated the library sources with the missing files.

It should work now.

All the best,

René

On 11 Feb 2015, at 18:11, Fedor Gusev <gusevfe@gmail.com> wrote:

Great news!

I've run into a problem though :(

If you download a package from from http://packages.seqan.de/seqan-library/seqan-library-2.0.0.tar.bz2 and define SEQAN_HAS_ZLIB, then 

#include "zipstream/zutil.h"

has effect. But the file is missing from the package, yet present in github repo. Is this intended?

On Wed, Feb 11, 2015 at 7:54 PM, Rahn, René <rene.maerker@fu-berlin.de> wrote:

Dear SeqAn-Users and Developers,

We are happy to announce the new release of SeqAn 2.0.0. 

We have many new features and applications for you and improved many parts in sense of usability, performance and stability.

For example, we have improved the usability and the performance of the I/O-modules. Now BAM-I/O supports parallel read and write operations. We improved automatic read/write operations for compressed file formats, like gzip, bzip2, etc..

We improved the performance of several data structures like the FMIndex, which runs now up to 4 times faster than the old version.

We extended the library with new features like the X-drop extensions for alignments allowing affine gap costs. We added a new realignment module as well as a translation module to translate amino acid alphabet into DNA alphabet.

We implemented many new apps like ANISE and BASIL for insert assembly, Fiona for read error correction, Yara an enhanced read aligner replacing Masai, and many many more.

With SeqAn 2.0.0 we moved the complete sources to GitHub, which enhances the development cycle in a great way. We improved our build system and added Continous Integration builds with Travis CI. We also updated and improved the API documentation (docs.seqan.de) and switched the tutorials to seqan.readthedocs.org.

You can download the new release and the updated apps from www.seqan.de in the downloads section. You can get the complete sources of the SeqAn 2.0.0 from https://github/seqan/seqan as well.

Simply run:

git clone -b seqan-v2.0.0 https://github.com/seqan/seqan.git seqan-src 

and start developing and having fun with SeqAn 2.0.0.

A note for SeqAn developers: 

Many modules are backward compatible with the old release, however, we also included some API changes to unify and improve the interfaces of some modules, like the I/O-modules. If you want to switch to the new release it is likely that you have to slightly adapt your application. You can use the API documentation (docs.seqan.de) and the tutorials (seqan.readthedocs.org) to learn more about new interfaces and adapted modules.  However, you can also keep track of the last stable release and update later if you want.

Simply run:

git clone -b seqan-v1.4.2 https://github.com/seqan/seqan.git seqan-src

to get a fresh clone or just switch to the correct branch within you existing clone:

git checkout tags/seqan-v1.4.2

and nothing changes for you.

We thank all people involved in the new release for their hard and awesome work.

Enjoy!

The SeqAn Team

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Kind regards,
Fedor Gusev.

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René Rahn

Ph.D. Student

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Tel:  (+49) 30 838 75277

Mail: rene.rahn@fu-berlin.de

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Institute of Computer Science

Algorithmic Bioinformatics (ABI)

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Freie Universität Berlin

Takustraße 9

14195 Berlin

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