From f.buske@uq.edu.au Thu Jul 29 13:32:49 2010 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1OeRLz-0001kN-Dc>; Thu, 29 Jul 2010 13:32:47 +0200 Received: from mail04.syd.optusnet.com.au ([211.29.132.185]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1OeRLy-0001QP-MQ>; Thu, 29 Jul 2010 13:32:47 +0200 Received: from Fabian-Buskes-MacBook.local (c122-108-178-120.rochd4.qld.optusnet.com.au [122.108.178.120]) by mail04.syd.optusnet.com.au (8.13.1/8.13.1) with ESMTP id o6TBWeov010528 for ; Thu, 29 Jul 2010 21:32:41 +1000 Message-ID: <4C5166D8.3010200@uq.edu.au> Date: Thu, 29 Jul 2010 21:32:40 +1000 From: Fabian Buske User-Agent: Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.1.9) Gecko/20100317 Thunderbird/3.0.4 MIME-Version: 1.0 To: SeqAn Development Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit X-Originating-IP: 211.29.132.185 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1280403167-000069FD-C57C3683/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Burundi.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.9 required=5.0 tests=FORGED_RCVD_HELO, RATWARE_GECKO_BUILD,SPF_HELO_PASS Subject: [Seqan-dev] Seeds and seed2 - which one for what X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 29 Jul 2010 11:32:49 -0000 Hi Seqan team, recently a seed2 directory was added to the seqan library in the svn. I was wondering what its story is. Is it going to replace the existing seed and seedset templates in the future? Should I switch my development to seed2? Is there any further support for the seed(1) templates (I figured that my reported bug+bugfix has not been incorporated into the library yet)? Speaking of the "standard" seedset template. The memory manager used to store the seeds still gives me a major headache especially when putting the seedsets into a skiplist and valgrind (http://cs.ecs.baylor.edu/~donahoo/tools/valgrind/) reports memory leaks (though there seems to be some funny things with pointers going on, which may confuse valgrind). The new seed2 template don't seem to rely the memory manager. So it looks natural to switch to the seed2 templates but I would first like to get a statement from the development team before I put any effort into adjusting my program. Looking forward to your comments. Cheers, Fabian From manuel.holtgrewe@fu-berlin.de Thu Jul 29 13:43:05 2010 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1OeRVw-00024X-G2>; Thu, 29 Jul 2010 13:43:04 +0200 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1OeRVw-0003Ce-Dw>; Thu, 29 Jul 2010 13:43:04 +0200 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by relay2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1OeRVw-0004uu-BC>; Thu, 29 Jul 2010 13:43:04 +0200 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by exchange6.fu-berlin.de ([160.45.9.133]) with mapi; Thu, 29 Jul 2010 13:42:48 +0200 From: "Holtgrewe, Manuel" To: SeqAn Development Date: Thu, 29 Jul 2010 13:43:03 +0200 Thread-Topic: [Seqan-dev] Seeds and seed2 - which one for what Thread-Index: AcsvEys81Pbe4FKGSF6FaqDHUg6XjA== Message-ID: <870EFB13-30BB-4C6F-9FCB-B3D3345AB948@fu-berlin.de> References: <4C5166D8.3010200@uq.edu.au> In-Reply-To: <4C5166D8.3010200@uq.edu.au> Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: acceptlanguage: en-US, de-DE Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Originating-IP: 160.45.9.133 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1280403784-000069FD-CC721D8F/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.012462, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Burundi.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: Re: [Seqan-dev] Seeds and seed2 - which one for what X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 29 Jul 2010 11:43:05 -0000 Hi Fabian, I am currently rewriting the seeds module. The code should not be considere= d stable in any form. If you are interested, I will send an email to you/th= is list when it is usable. Bests, Manuel=