From charles-listes+seqan@plessy.org Tue Sep 06 16:17:47 2011 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 <1R0wTB-00065U-Ur>; Tue, 06 Sep 2011 16:17:46 +0200 Received: from x122082.ppp.asahi-net.or.jp ([122.249.122.82] helo=mail.plessy.org) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1R0wTB-0007RX-Ip>; Tue, 06 Sep 2011 16:17:45 +0200 Received: from merveille.plessy.net (merveille.igloo [192.168.0.1]) by mail.plessy.org (Postfix) with ESMTPSA id 90134156154 for ; Tue, 6 Sep 2011 23:11:56 +0900 (JST) Date: Tue, 6 Sep 2011 23:11:53 +0900 From: Charles Plessy To: seqan-dev@lists.fu-berlin.de Message-ID: <20110906141141.GA9339@merveille.plessy.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Disposition: inline Content-Transfer-Encoding: 8bit User-Agent: Mutt/1.5.20 (2009-06-14) X-Originating-IP: 122.249.122.82 X-ZEDAT-Hint: G X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1315318665-00005A17-75083851/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.001277, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Algerien.ZEDAT.FU-Berlin.DE X-Spam-Level: xx X-Spam-Status: No, score=2.5 required=5.0 tests=FORGED_RCVD_HELO,FU_XZH_G Subject: [Seqan-dev] No rule to make target `razers/paramChooser' ? 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: Tue, 06 Sep 2011 14:17:47 -0000 Dear SeqAn developers, when trying to compile the SeqAn 1.3 applications using ‘make’ in the apps directory, I encounter the following error. g++ -I.. -O9 -fopenmp -march=native -DSEQAN_ENABLE_DEBUG=0 -pedantic -W -Wall -Wno-variadic-macros -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_ENABLE_TESTING=0 -static -lrt seqcons/seqcons.cpp -o seqcons/seqcons make: *** No rule to make target `razers/paramChooser', needed by `all'. Stop. If I delete the razers/paramChooser target, the compilation goes fine. I am not sure what to do… This is to update the sequan package distributed in Debian, as discussed in our bug tracker: http://bugs.debian.org/640302 The simple command ‘cd apps && make’ worked correctly for version 1.2. Could you give us an advice ? Have a nice day, -- Charles Plessy Debian Med packaging team http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan From manuel.holtgrewe@fu-berlin.de Tue Sep 06 21:45:33 2011 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 <1R11aO-0001OQ-2f>; Tue, 06 Sep 2011 21:45:32 +0200 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost1.zedat.fu-berlin.de (Exim 4.69) with esmtp (envelope-from ) id <1R11aO-0006E3-0Q>; Tue, 06 Sep 2011 21:45:32 +0200 Received: from 91-65-212-104-dynip.superkabel.de ([91.65.212.104] helo=[192.168.0.100]) by inpost2.zedat.fu-berlin.de (Exim 4.69) with esmtpsa (envelope-from ) id <1R11aN-0003m4-UE>; Tue, 06 Sep 2011 21:45:32 +0200 Message-Id: <4F685AB3-073D-4889-9C7F-2427BEB4D479@fu-berlin.de> From: Manuel Holtgrewe To: SeqAn Development In-Reply-To: <20110906141141.GA9339@merveille.plessy.net> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Content-Transfer-Encoding: 7bit Mime-Version: 1.0 (Apple Message framework v936) Date: Tue, 6 Sep 2011 21:45:24 +0200 References: <20110906141141.GA9339@merveille.plessy.net> X-Mailer: Apple Mail (2.936) X-Originating-IP: 91.65.212.104 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1315338332-00005A17-33A01F22/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.050387, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Algerien.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: Re: [Seqan-dev] No rule to make target `razers/paramChooser' ? 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: Tue, 06 Sep 2011 19:45:33 -0000 Charles, we have dropped the old build system in favour of CMake. You can find documentation on building for 1.3 here (note the ? version=27 for 1.3 instructions): http://trac.mi.fu-berlin.de/seqan/wiki/Tutorial/GettingStarted?version=27 Note that in the upcoming 1.4 version (hopefully released later this year), the exact instructions will differ and you will be able to find them here (no ?version, most current wiki page): http://trac.mi.fu-berlin.de/seqan/wiki/Tutorial/GettingStarted HTH Manuel From bernd.jagla@pasteur.fr Thu Sep 15 14:38:05 2011 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 <1R4BCe-0008E6-Bd>; Thu, 15 Sep 2011 14:38:04 +0200 Received: from mail-interne3.pasteur.fr ([157.99.64.82]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1R4BCe-0003nA-8O>; Thu, 15 Sep 2011 14:38:04 +0200 Received: from maroilles.sis.pasteur.fr (localhost [127.0.0.1]) by mail-interne3.pasteur.fr (Postfix) with ESMTP id 31BD0381055 for ; Thu, 15 Sep 2011 14:38:03 +0200 (CEST) X-Virus-Scanned: amavisd-new at pasteur.fr Received: from [127.0.0.1] (zillumina.pt2.pasteur.fr [157.99.241.40]) by mail-interne3.pasteur.fr (Postfix) with ESMTP id E4BEF38104C for ; Thu, 15 Sep 2011 14:38:02 +0200 (CEST) Message-ID: <4E71F1AA.6020808@pasteur.fr> Date: Thu, 15 Sep 2011 14:38:02 +0200 From: Bernd Jagla User-Agent: Mozilla/5.0 (Windows NT 5.1; rv:6.0.2) Gecko/20110902 Thunderbird/6.0.2 MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Originating-IP: 157.99.64.82 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1316090284-00005A17-2C326843/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.393700, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Gabun.ZEDAT.FU-Berlin.DE X-Spam-Level: xx X-Spam-Status: No, score=2.2 required=5.0 tests=DNS_FROM_RFC_POST, RATWARE_GECKO_BUILD Subject: [Seqan-dev] bgzf question 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, 15 Sep 2011 12:38:05 -0000 Hi, I would like to ask our sysadmins to install the bgzf libraries necessary for reading the bam files. could you please let me know how the libraries are called? I am working on a Linux/Redhat 64 bit machine. the reason why I believe we don't have that library is because I see the following error messages during linking: /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/extras/include/seqan/ext_lh3/bgzf-impl.h:316: undefined reference to `deflateInit2_' and may more of this kind... Thanks for your kind help, Bernd From manuel.holtgrewe@fu-berlin.de Thu Sep 15 14:57:35 2011 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 <1R4BVW-0000Wl-C2>; Thu, 15 Sep 2011 14:57:34 +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 <1R4BVW-0002vH-AD>; Thu, 15 Sep 2011 14:57:34 +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 <1R4BVW-00063P-4j>; Thu, 15 Sep 2011 14:57:34 +0200 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by exchange6.fu-berlin.de ([160.45.9.133]) with mapi; Thu, 15 Sep 2011 14:57:33 +0200 From: "Holtgrewe, Manuel" To: SeqAn Development Date: Thu, 15 Sep 2011 14:57:32 +0200 Thread-Topic: [Seqan-dev] bgzf question Thread-Index: Acxzpwi3DYptZnf3TRadde3FQGuJaw== Message-ID: <8E9C49CA-5AE6-4C30-A866-E30418578233@fu-berlin.de> References: <4E71F1AA.6020808@pasteur.fr> In-Reply-To: <4E71F1AA.6020808@pasteur.fr> 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::1316091454-00005A17-57161206/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.021226, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Dschibuti.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: Re: [Seqan-dev] bgzf question 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, 15 Sep 2011 12:57:35 -0000 Bernd, the bgzf libraries are included with SeqAn. The only thing you need is zlib= . On some Linux systems, you need the "developer version" which includes the = headers. Check if /usr/include/zlib.h already exists. If this is the case (= 99% of all Linux installations will feature this) then you should be good t= o go already. Bests, Manuel Am 15.09.2011 um 14:38 schrieb Bernd Jagla: > Hi, >=20 > I would like to ask our sysadmins to install the bgzf libraries=20 > necessary for reading the bam files. > could you please let me know how the libraries are called? I am working=20 > on a Linux/Redhat 64 bit machine. >=20 > the reason why I believe we don't have that library is because I see the= =20 > following error messages during linking: >=20 > /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/extras/incl= ude/seqan/ext_lh3/bgzf-impl.h:316:=20 > undefined reference to `deflateInit2_' >=20 > and may more of this kind... >=20 > Thanks for your kind help, >=20 > Bernd >=20 >=20 > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev From bernd.jagla@pasteur.fr Mon Sep 26 15:19:10 2011 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 <1R8B5S-0006Mn-2z>; Mon, 26 Sep 2011 15:19:10 +0200 Received: from mail-interne3.pasteur.fr ([157.99.64.82]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1R8B5R-0004sK-Vl>; Mon, 26 Sep 2011 15:19:10 +0200 Received: from maroilles.sis.pasteur.fr (localhost [127.0.0.1]) by mail-interne3.pasteur.fr (Postfix) with ESMTP id 118B638104F for ; Mon, 26 Sep 2011 15:19:09 +0200 (CEST) X-Virus-Scanned: amavisd-new at pasteur.fr Received: from [127.0.0.1] (zillumina.pt2.pasteur.fr [157.99.241.40]) by mail-interne3.pasteur.fr (Postfix) with ESMTP id C946238104C for ; Mon, 26 Sep 2011 15:19:08 +0200 (CEST) Message-ID: <4E807BCE.4070606@pasteur.fr> Date: Mon, 26 Sep 2011 15:19:10 +0200 From: Bernd Jagla User-Agent: Mozilla/5.0 (Windows NT 5.1; rv:6.0.2) Gecko/20110902 Thunderbird/6.0.2 MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Originating-IP: 157.99.64.82 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1317043150-00005A17-E57CE997/0-0/0-0 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: xx X-Spam-Status: No, score=2.2 required=5.0 tests=DNS_FROM_RFC_POST, RATWARE_GECKO_BUILD Subject: [Seqan-dev] reading in fastq file with read not read2 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: Mon, 26 Sep 2011 13:19:11 -0000 Hi, I would like to read a fastQ file with a single pass record by record and not store the sequences in memory. I only found read2 sample, which reads everything into memory (I believe).... Could you please enlighten me on how to do that or where to find more information about that? Thanks, Bernd From manuel.holtgrewe@fu-berlin.de Mon Sep 26 15:32:32 2011 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 <1R8BIN-0006qZ-Hf>; Mon, 26 Sep 2011 15:32:31 +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 <1R8BIN-0001NP-FM>; Mon, 26 Sep 2011 15:32:31 +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 <1R8BIN-0002dQ-9e>; Mon, 26 Sep 2011 15:32:31 +0200 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by exchange6.fu-berlin.de ([160.45.9.133]) with mapi; Mon, 26 Sep 2011 15:32:31 +0200 From: "Holtgrewe, Manuel" To: SeqAn Development Date: Mon, 26 Sep 2011 15:32:30 +0200 Thread-Topic: [Seqan-dev] reading in fastq file with read not read2 Thread-Index: Acx8UL1TTfGBSmHpQMW/LbAVLbwMAQ== Message-ID: <9F69C9E4-C9B1-403E-918A-CD2778123282@fu-berlin.de> References: <4E807BCE.4070606@pasteur.fr> In-Reply-To: <4E807BCE.4070606@pasteur.fr> 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::1317043951-00005A17-DCF1D1A1/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000048, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Algerien.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: Re: [Seqan-dev] reading in fastq file with read not read2 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: Mon, 26 Sep 2011 13:32:32 -0000 Bernd, good catch! For some reason, the Record Reading API demo from the tutorial = was overwritten with opening compressed files. I just fixed this and you ca= n now find the example here: http://trac.mi.fu-berlin.de/seqan/wiki/Tutorial/ReadingSequenceFiles#Record= ReadingAPI Thanks, Manuel Am 26.09.2011 um 15:19 schrieb Bernd Jagla: > Hi, >=20 > I would like to read a fastQ file with a single pass record by record=20 > and not store the sequences in memory. > I only found read2 sample, which reads everything into memory (I=20 > believe).... >=20 > Could you please enlighten me on how to do that or where to find more=20 > information about that? >=20 > Thanks, >=20 > Bernd >=20 >=20 > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev From bernd.jagla@pasteur.fr Mon Sep 26 15:54:33 2011 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 <1R8Bdf-0007eu-45>; Mon, 26 Sep 2011 15:54:31 +0200 Received: from mail-interne3.pasteur.fr ([157.99.64.82]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1R8Bdf-0006gw-0p>; Mon, 26 Sep 2011 15:54:31 +0200 Received: from maroilles.sis.pasteur.fr (localhost [127.0.0.1]) by mail-interne3.pasteur.fr (Postfix) with ESMTP id 9EF0238105C for ; Mon, 26 Sep 2011 15:54:30 +0200 (CEST) X-Virus-Scanned: amavisd-new at pasteur.fr Received: from [127.0.0.1] (zillumina.pt2.pasteur.fr [157.99.241.40]) by mail-interne3.pasteur.fr (Postfix) with ESMTP id 5DFCC38105E for ; Mon, 26 Sep 2011 15:54:30 +0200 (CEST) Message-ID: <4E80840E.3000908@pasteur.fr> Date: Mon, 26 Sep 2011 15:54:22 +0200 From: Bernd Jagla User-Agent: Mozilla/5.0 (Windows NT 5.1; rv:6.0.2) Gecko/20110902 Thunderbird/6.0.2 MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de References: <4E807BCE.4070606@pasteur.fr> <9F69C9E4-C9B1-403E-918A-CD2778123282@fu-berlin.de> In-Reply-To: <9F69C9E4-C9B1-403E-918A-CD2778123282@fu-berlin.de> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Originating-IP: 157.99.64.82 X-purgate: suspect X-purgate-type: suspect X-purgate-ID: 151147::1317045271-00005A17-483D7F63/3430351984-0/0-1 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 Botsuana.ZEDAT.FU-Berlin.DE X-Spam-Level: xxx X-Spam-Status: No, score=3.2 required=5.0 tests=DNS_FROM_RFC_POST, FU_XPURGATE_SUSP,RATWARE_GECKO_BUILD Subject: Re: [Seqan-dev] reading in fastq file with read not read2 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: Mon, 26 Sep 2011 13:54:33 -0000 thanks, it seems that the corresponding file is also not there: http://trac.mi.fu-berlin.de/seqan/browser/trunk/seqan/extras/demos/tutorial/stream/stream_read_fasta.cpp Thanks, Bernd On 9/26/2011 3:32 PM, Holtgrewe, Manuel wrote: > Bernd, > > good catch! For some reason, the Record Reading API demo from the tutorial was overwritten with opening compressed files. I just fixed this and you can now find the example here: > > http://trac.mi.fu-berlin.de/seqan/wiki/Tutorial/ReadingSequenceFiles#RecordReadingAPI > > Thanks, > Manuel > > Am 26.09.2011 um 15:19 schrieb Bernd Jagla: > >> Hi, >> >> I would like to read a fastQ file with a single pass record by record >> and not store the sequences in memory. >> I only found read2 sample, which reads everything into memory (I >> believe).... >> >> Could you please enlighten me on how to do that or where to find more >> information about that? >> >> Thanks, >> >> Bernd >> >> >> _______________________________________________ >> seqan-dev mailing list >> seqan-dev@lists.fu-berlin.de >> https://lists.fu-berlin.de/listinfo/seqan-dev > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev > > From bernd.jagla@pasteur.fr Mon Sep 26 16:30:59 2011 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 <1R8CCx-0000dA-1D>; Mon, 26 Sep 2011 16:30:59 +0200 Received: from mail-interne3.pasteur.fr ([157.99.64.82]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1R8CCw-0001ZK-Sx>; Mon, 26 Sep 2011 16:30:59 +0200 Received: from maroilles.sis.pasteur.fr (localhost [127.0.0.1]) by mail-interne3.pasteur.fr (Postfix) with ESMTP id BBDA938104F for ; Mon, 26 Sep 2011 16:30:57 +0200 (CEST) X-Virus-Scanned: amavisd-new at pasteur.fr Received: from [127.0.0.1] (zillumina.pt2.pasteur.fr [157.99.241.40]) by mail-interne3.pasteur.fr (Postfix) with ESMTP id 9886838104C for ; Mon, 26 Sep 2011 16:30:57 +0200 (CEST) Message-ID: <4E808CA3.8080304@pasteur.fr> Date: Mon, 26 Sep 2011 16:30:59 +0200 From: Bernd Jagla User-Agent: Mozilla/5.0 (Windows NT 5.1; rv:6.0.2) Gecko/20110902 Thunderbird/6.0.2 MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de Content-Type: text/plain; charset=windows-1252; format=flowed Content-Transfer-Encoding: 8bit X-Originating-IP: 157.99.64.82 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1317047459-00005A17-4B25A286/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.007433, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Benin.ZEDAT.FU-Berlin.DE X-Spam-Level: xx X-Spam-Status: No, score=2.2 required=5.0 tests=DNS_FROM_RFC_POST, RATWARE_GECKO_BUILD Subject: [Seqan-dev] i am lost again 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: Mon, 26 Sep 2011 14:31:00 -0000 Sorry for these naive questions... I am running into problems with a simple program to read in fastq data. I am trying to use the samples/demos that you provide... In short I am getting the following error message: make readCleansing Building file: ../src/readCleansing.cpp Invoking: GCC C++ Compiler g++ -DSEQAN_ENABLE_DEBUG=1 -DSEQAN_HAS_ZLIB=1 -I/pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/include -I/pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/extras/include -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/readCleansing.d" -MT"src/readCleansing.d" -o "src/readCleansing.o" "../src/readCleansing.cpp" ../src/readCleansing.cpp: In function ‘int main(int, const char**)’: ../src/readCleansing.cpp:299: error: no matching function for call to ‘std::basic_ifstream >::basic_ifstream(seqan::CharString&, std::_Ios_Openmode)’ /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream:442: note: candidates are: std::basic_ifstream<_CharT, _Traits>::basic_ifstream(const char*, std::_Ios_Openmode) [with _CharT = char, _Traits = std::char_traits] /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream:428: note: std::basic_ifstream<_CharT, _Traits>::basic_ifstream() [with _CharT = char, _Traits = std::char_traits] /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd:89: note: std::basic_ifstream >::basic_ifstream(const std::basic_ifstream >&) make: *** [src/readCleansing.o] Error 1 The offending code looks like this: std::ifstream fasta(options.inFile, std::ios_base::in | std::ios_base::binary); if (!fasta.good()) return 1; RecordReader > reader(fasta); I have tried to exchange fasta with fastq, but though I believe that is what I really want it is not the real problem... As I am a novice to C++ and I appologize for the naive questions... Please let me know if you need further information for identifying the problem... PS. Other programs compile correctly Thanks, Bernd From manuel.holtgrewe@fu-berlin.de Mon Sep 26 17:36:15 2011 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 <1R8DE6-000347-8u>; Mon, 26 Sep 2011 17:36:14 +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 <1R8DE6-00077b-6j>; Mon, 26 Sep 2011 17:36:14 +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 <1R8DE6-0006C7-1Q>; Mon, 26 Sep 2011 17:36:14 +0200 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by exchange6.fu-berlin.de ([160.45.9.133]) with mapi; Mon, 26 Sep 2011 17:36:14 +0200 From: "Holtgrewe, Manuel" To: SeqAn Development Date: Mon, 26 Sep 2011 17:36:12 +0200 Thread-Topic: [Seqan-dev] reading in fastq file with read not read2 Thread-Index: Acx8YgXb080jYfmsQrSU/e0TsB8Hvw== Message-ID: <8C2D1876-ABD9-425D-A19B-E98C0DF6FF8B@fu-berlin.de> References: <4E807BCE.4070606@pasteur.fr> <9F69C9E4-C9B1-403E-918A-CD2778123282@fu-berlin.de> <4E80840E.3000908@pasteur.fr> In-Reply-To: <4E80840E.3000908@pasteur.fr> 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::1317051374-00005A17-3CE17EEB/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000007, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Algerien.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: Re: [Seqan-dev] reading in fastq file with read not read2 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: Mon, 26 Sep 2011 15:36:15 -0000 Try this one ;) I also updated the reference in the tutorial. http://trac.mi.fu-berlin.de/seqan/browser/trunk/seqan/extras/demos/tutorial= /stream/stream_read_record_fasta.cpp Am 26.09.2011 um 15:54 schrieb Bernd Jagla: > thanks, > it seems that the corresponding file is also not there: > http://trac.mi.fu-berlin.de/seqan/browser/trunk/seqan/extras/demos/tutori= al/stream/stream_read_fasta.cpp >=20 > Thanks, >=20 > Bernd >=20 > On 9/26/2011 3:32 PM, Holtgrewe, Manuel wrote: >> Bernd, >>=20 >> good catch! For some reason, the Record Reading API demo from the tutori= al was overwritten with opening compressed files. I just fixed this and you= can now find the example here: >>=20 >> http://trac.mi.fu-berlin.de/seqan/wiki/Tutorial/ReadingSequenceFiles#Rec= ordReadingAPI >>=20 >> Thanks, >> Manuel >>=20 >> Am 26.09.2011 um 15:19 schrieb Bernd Jagla: >>=20 >>> Hi, >>>=20 >>> I would like to read a fastQ file with a single pass record by record >>> and not store the sequences in memory. >>> I only found read2 sample, which reads everything into memory (I >>> believe).... >>>=20 >>> Could you please enlighten me on how to do that or where to find more >>> information about that? >>>=20 >>> Thanks, >>>=20 >>> Bernd >>>=20 >>>=20 >>> _______________________________________________ >>> seqan-dev mailing list >>> seqan-dev@lists.fu-berlin.de >>> https://lists.fu-berlin.de/listinfo/seqan-dev >>=20 >> _______________________________________________ >> seqan-dev mailing list >> seqan-dev@lists.fu-berlin.de >> https://lists.fu-berlin.de/listinfo/seqan-dev >>=20 >>=20 >=20 >=20 > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev From manuel.holtgrewe@fu-berlin.de Mon Sep 26 17:38:56 2011 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 <1R8DGh-00038o-8n>; Mon, 26 Sep 2011 17:38:55 +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 <1R8DGh-0007X3-6q>; Mon, 26 Sep 2011 17:38:55 +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 <1R8DGh-0006P3-1h>; Mon, 26 Sep 2011 17:38:55 +0200 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by exchange6.fu-berlin.de ([160.45.9.133]) with mapi; Mon, 26 Sep 2011 17:38:55 +0200 From: "Holtgrewe, Manuel" To: SeqAn Development Date: Mon, 26 Sep 2011 17:38:53 +0200 Thread-Topic: [Seqan-dev] i am lost again Thread-Index: Acx8YmXBDGII296ESXSCmzqfiX9WCw== Message-ID: <6B57A877-C9FF-4C8C-8AB8-1B2E6C99DA06@fu-berlin.de> References: <4E808CA3.8080304@pasteur.fr> In-Reply-To: <4E808CA3.8080304@pasteur.fr> 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="Windows-1252" 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::1317051535-00005A17-DD7E235F/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.009367, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Dschibuti.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: Re: [Seqan-dev] i am lost again 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: Mon, 26 Sep 2011 15:38:56 -0000 The offending line is: > std::ifstream fasta(options.inFile, > std::ios_base::in | std::ios_base::binary); The ifstream from the STL does not know about SeqAn Strings (which is the t= ype of options.inFile). Try this instead: std::ifstream fasta(toCString(options.inFile), std::ios_base::in | std::ios= _base::binary); Am 26.09.2011 um 16:30 schrieb Bernd Jagla: > Sorry for these naive questions... >=20 > I am running into problems with a simple program to read in fastq data.=20 > I am trying to use the samples/demos that you provide... >=20 > In short I am getting the following error message: >=20 > make readCleansing > Building file: ../src/readCleansing.cpp > Invoking: GCC C++ Compiler > g++ -DSEQAN_ENABLE_DEBUG=3D1 -DSEQAN_HAS_ZLIB=3D1=20 > -I/pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/incl= ude=20 > -I/pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/extras/in= clude=20 > -O3 -g3 -Wall -c -fmessage-length=3D0 -MMD -MP -MF"src/readCleansing.d"=20 > -MT"src/readCleansing.d" -o "src/readCleansing.o" "../src/readCleansing.c= pp" > ../src/readCleansing.cpp: In function =91int main(int, const char**)=92: > ../src/readCleansing.cpp:299: error: no matching function for call to=20 > =91std::basic_ifstream=20 >> ::basic_ifstream(seqan::CharString&, std::_Ios_Openmode)=92 > /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstr= eam:442:=20 > note: candidates are: std::basic_ifstream<_CharT,=20 > _Traits>::basic_ifstream(const char*, std::_Ios_Openmode) [with _CharT = =3D=20 > char, _Traits =3D std::char_traits] > /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstr= eam:428:=20 > note: std::basic_ifstream<_CharT, _Traits>::basic_ifstream() [with=20 > _CharT =3D char, _Traits =3D std::char_traits] > /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosf= wd:89:=20 > note: std::basic_ifstream=20 >> ::basic_ifstream(const std::basic_ifstream std::char_traits >&) > make: *** [src/readCleansing.o] Error 1 >=20 > The offending code looks like this: >=20 > std::ifstream fasta(options.inFile, > std::ios_base::in | std::ios_base::binary); > if (!fasta.good()) > return 1; > RecordReader > reader(fasta); >=20 >=20 > I have tried to exchange fasta with fastq, but though I believe that is=20 > what I really want it is not the real problem... >=20 > As I am a novice to C++ and I appologize for the naive questions... >=20 > Please let me know if you need further information for identifying the=20 > problem... >=20 > PS. Other programs compile correctly >=20 > Thanks, >=20 > Bernd >=20 >=20 >=20 >=20 > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev From bernd.jagla@pasteur.fr Tue Sep 27 08:13:30 2011 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 <1R8Qv2-0002Pf-SE>; Tue, 27 Sep 2011 08:13:28 +0200 Received: from mail-interne3.pasteur.fr ([157.99.64.82]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1R8Qv2-0007xJ-Nu>; Tue, 27 Sep 2011 08:13:28 +0200 Received: from maroilles.sis.pasteur.fr (localhost [127.0.0.1]) by mail-interne3.pasteur.fr (Postfix) with ESMTP id 44E82381050 for ; Tue, 27 Sep 2011 08:13:28 +0200 (CEST) X-Virus-Scanned: amavisd-new at pasteur.fr Received: from [127.0.0.1] (zillumina.pt2.pasteur.fr [157.99.241.40]) by mail-interne3.pasteur.fr (Postfix) with ESMTP id 1DD3E38104C for ; Tue, 27 Sep 2011 08:13:28 +0200 (CEST) Message-ID: <4E81698A.6050808@pasteur.fr> Date: Tue, 27 Sep 2011 08:13:30 +0200 From: Bernd Jagla User-Agent: Mozilla/5.0 (Windows NT 5.1; rv:6.0.2) Gecko/20110902 Thunderbird/6.0.2 MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de References: <4E808CA3.8080304@pasteur.fr> <6B57A877-C9FF-4C8C-8AB8-1B2E6C99DA06@fu-berlin.de> In-Reply-To: <6B57A877-C9FF-4C8C-8AB8-1B2E6C99DA06@fu-berlin.de> Content-Type: text/plain; charset=windows-1252; format=flowed Content-Transfer-Encoding: 8bit X-Originating-IP: 157.99.64.82 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1317104008-00005A17-12BA9BF0/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.016566, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Botsuana.ZEDAT.FU-Berlin.DE X-Spam-Level: xx X-Spam-Status: No, score=2.2 required=5.0 tests=DNS_FROM_RFC_POST, RATWARE_GECKO_BUILD Subject: Re: [Seqan-dev] i am lost again 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: Tue, 27 Sep 2011 06:13:30 -0000 Great that works. Don't know how I could have come up with this solution... I guess I need A LOT more C++ experience... So beware of more of these questions.... By the way... I am now looking into how to access a character from a string (CharString/Dna5String) and do position based comparisons... But I will ask if I won't find anything on the net... Thanks again, Bernd On 9/26/2011 5:38 PM, Holtgrewe, Manuel wrote: > The offending line is: > >> std::ifstream fasta(options.inFile, >> std::ios_base::in | std::ios_base::binary); > The ifstream from the STL does not know about SeqAn Strings (which is the type of options.inFile). > > Try this instead: > > std::ifstream fasta(toCString(options.inFile), std::ios_base::in | std::ios_base::binary); > > > Am 26.09.2011 um 16:30 schrieb Bernd Jagla: > >> Sorry for these naive questions... >> >> I am running into problems with a simple program to read in fastq data. >> I am trying to use the samples/demos that you provide... >> >> In short I am getting the following error message: >> >> make readCleansing >> Building file: ../src/readCleansing.cpp >> Invoking: GCC C++ Compiler >> g++ -DSEQAN_ENABLE_DEBUG=1 -DSEQAN_HAS_ZLIB=1 >> -I/pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/include >> -I/pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/extras/include >> -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/readCleansing.d" >> -MT"src/readCleansing.d" -o "src/readCleansing.o" "../src/readCleansing.cpp" >> ../src/readCleansing.cpp: In function ‘int main(int, const char**)’: >> ../src/readCleansing.cpp:299: error: no matching function for call to >> ‘std::basic_ifstream >>> ::basic_ifstream(seqan::CharString&, std::_Ios_Openmode)’ >> /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream:442: >> note: candidates are: std::basic_ifstream<_CharT, >> _Traits>::basic_ifstream(const char*, std::_Ios_Openmode) [with _CharT = >> char, _Traits = std::char_traits] >> /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream:428: >> note: std::basic_ifstream<_CharT, _Traits>::basic_ifstream() [with >> _CharT = char, _Traits = std::char_traits] >> /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd:89: >> note: std::basic_ifstream >>> ::basic_ifstream(const std::basic_ifstream> std::char_traits >&) >> make: *** [src/readCleansing.o] Error 1 >> >> The offending code looks like this: >> >> std::ifstream fasta(options.inFile, >> std::ios_base::in | std::ios_base::binary); >> if (!fasta.good()) >> return 1; >> RecordReader > reader(fasta); >> >> >> I have tried to exchange fasta with fastq, but though I believe that is >> what I really want it is not the real problem... >> >> As I am a novice to C++ and I appologize for the naive questions... >> >> Please let me know if you need further information for identifying the >> problem... >> >> PS. Other programs compile correctly >> >> Thanks, >> >> Bernd >> >> >> >> >> _______________________________________________ >> seqan-dev mailing list >> seqan-dev@lists.fu-berlin.de >> https://lists.fu-berlin.de/listinfo/seqan-dev > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev > >