From manuel.holtgrewe@fu-berlin.de Mon Dec 05 18:31:39 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 <1RXcO9-0004sk-DV>; Mon, 05 Dec 2011 18:31:37 +0100 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 <1RXcO9-0002qT-BK>; Mon, 05 Dec 2011 18:31:37 +0100 Received: from ecoli.imp.fu-berlin.de ([160.45.111.133]) by inpost2.zedat.fu-berlin.de (Exim 4.69) with esmtpsa (envelope-from ) id <1RXcO9-0004aU-9G>; Mon, 05 Dec 2011 18:31:37 +0100 Message-ID: <4EDCFFD5.3020902@fu-berlin.de> Date: Mon, 05 Dec 2011 18:31:01 +0100 From: Manuel Holtgrewe User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:8.0) Gecko/20111124 Thunderbird/8.0 MIME-Version: 1.0 To: agabi@mi.fu-berlin.de, SeqAn Development Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Originating-IP: 160.45.111.133 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1323106297-000067B8-C1C734A2/0-0/0-0 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=-2.0 required=5.0 tests=ALL_TRUSTED, RATWARE_GECKO_BUILD Subject: [Seqan-dev] SeqAn Trac has moved 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, 05 Dec 2011 17:31:39 -0000 Dear all, after upgrading our Trac instance, we have moved it now to http://trac.seqan.de/. Sorry for any inconvenience, Manuel From bakaric@evolbio.mpg.de Tue Dec 06 10:06:10 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 <1RXqyW-0008MI-6N>; Tue, 06 Dec 2011 10:06:08 +0100 Received: from zimbra.evolbio.mpg.de ([141.5.8.20]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RXqyW-0003MV-3o>; Tue, 06 Dec 2011 10:06:08 +0100 Received: from localhost (localhost [127.0.0.1]) by zimbra.evolbio.mpg.de (Postfix) with ESMTP id A04CC2CFA76C for ; Tue, 6 Dec 2011 10:05:26 +0100 (CET) X-Virus-Scanned: amavisd-new at zimbra.evolbio.mpg.de Received: from zimbra.evolbio.mpg.de ([127.0.0.1]) by localhost (zimbra.evolbio.mpg.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id YE6BxBg0xzM9 for ; Tue, 6 Dec 2011 10:05:26 +0100 (CET) Received: from zimbra.evolbio.mpg.de (zimbra.evolbio.mpg.de [172.16.255.20]) by zimbra.evolbio.mpg.de (Postfix) with ESMTP id 41A392CFA765 for ; Tue, 6 Dec 2011 10:05:25 +0100 (CET) Date: Tue, 06 Dec 2011 10:03:20 +0100 (CET) From: Robert Bakaric To: seqan-dev@lists.fu-berlin.de Message-ID: <388e1f57-84f6-41c5-adaf-82a55cfdc5eb@zimbra> In-Reply-To: <57969599-8278-42b4-83ca-c8567da2a45b@zimbra> Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 7bit MIME-Version: 1.0 X-Mailer: Zimbra 7.1.3_GA_3346 (ZimbraWebClient - FF3.0 (Linux)/7.1.3_GA_3346) X-Originating-IP: 141.5.8.20 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1323162368-000067B8-53E8822C/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.014076, 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=0.0 required=5.0 tests=none Subject: [Seqan-dev] Getting started with SeqAn 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 Dec 2011 09:06:10 -0000 Hello, I have a simple starter question. So I have downloaded the seqan and followed the instruction on "getting started": http://trac.seqan.de/wiki/Tutorial/GettingStarted , and that worked. but now i have tried to make some demos and i got the following message: $ cmake2.8.6 . CMake Error at CMakeLists.txt:4 (seqan_setup_apps): Unknown CMake command "seqan_setup_apps". -- Configuring incomplete, errors occurred! I'm probably missing something obvious but, don't see it.. My OS: Ubuntu 10.04 g++ (Ubuntu 4.4.3-4ubuntu5) 4.4.3 cmake version 2.8.6 Thank you, Robert From bakaric@evolbio.mpg.de Tue Dec 06 10:07:01 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 <1RXqzM-0008Mn-Ez>; Tue, 06 Dec 2011 10:07:00 +0100 Received: from zimbra.evolbio.mpg.de ([141.5.8.20]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RXqzM-0003RF-CM>; Tue, 06 Dec 2011 10:07:00 +0100 Received: from localhost (localhost [127.0.0.1]) by zimbra.evolbio.mpg.de (Postfix) with ESMTP id 829682CFA75F for ; Tue, 6 Dec 2011 10:06:48 +0100 (CET) X-Virus-Scanned: amavisd-new at zimbra.evolbio.mpg.de Received: from zimbra.evolbio.mpg.de ([127.0.0.1]) by localhost (zimbra.evolbio.mpg.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 5QiOL0uvAWws for ; Tue, 6 Dec 2011 10:06:48 +0100 (CET) Received: from zimbra.evolbio.mpg.de (zimbra.evolbio.mpg.de [172.16.255.20]) by zimbra.evolbio.mpg.de (Postfix) with ESMTP id 834672CFA75B for ; Tue, 6 Dec 2011 10:06:47 +0100 (CET) Date: Tue, 06 Dec 2011 10:06:22 +0100 (CET) From: Robert Bakaric To: seqan-dev@lists.fu-berlin.de Message-ID: <6a6a3656-5fc7-4b78-929a-d8da2232ba49@zimbra> In-Reply-To: <57969599-8278-42b4-83ca-c8567da2a45b@zimbra> Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 7bit MIME-Version: 1.0 X-Mailer: Zimbra 7.1.3_GA_3346 (ZimbraWebClient - FF3.0 (Linux)/7.1.3_GA_3346) X-Originating-IP: 141.5.8.20 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1323162420-000067B8-C934B332/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.014076, 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=0.0 required=5.0 tests=none Subject: [Seqan-dev] Getting started with SeqAn 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 Dec 2011 09:07:01 -0000 Hello, I have a simple starter question. So I have downloaded the seqan and followed the instruction on "getting started": http://trac.seqan.de/wiki/Tutorial/GettingStarted , and that worked. but now i have tried to make some demos and i got the following message: $ cmake2.8.6 . CMake Error at CMakeLists.txt:4 (seqan_setup_apps): Unknown CMake command "seqan_setup_apps". -- Configuring incomplete, errors occurred! I'm probably missing something obvious but, don't see it.. My OS: Ubuntu 10.04 g++ (Ubuntu 4.4.3-4ubuntu5) 4.4.3 cmake version 2.8.6 Thank you, Robert From manuel.holtgrewe@fu-berlin.de Tue Dec 06 12:44:09 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 <1RXtRP-0005mV-56>; Tue, 06 Dec 2011 12:44:07 +0100 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 <1RXtRP-0006kt-33>; Tue, 06 Dec 2011 12:44:07 +0100 Received: from ecoli.imp.fu-berlin.de ([160.45.111.133]) by inpost2.zedat.fu-berlin.de (Exim 4.69) with esmtpsa (envelope-from ) id <1RXtRP-0001pR-0w>; Tue, 06 Dec 2011 12:44:07 +0100 Message-ID: <4EDDFFE2.6020809@fu-berlin.de> Date: Tue, 06 Dec 2011 12:43:30 +0100 From: Manuel Holtgrewe User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:8.0) Gecko/20111124 Thunderbird/8.0 MIME-Version: 1.0 To: SeqAn Development References: <6a6a3656-5fc7-4b78-929a-d8da2232ba49@zimbra> In-Reply-To: <6a6a3656-5fc7-4b78-929a-d8da2232ba49@zimbra> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Originating-IP: 160.45.111.133 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1323171847-000067B8-31E3FC5A/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000001, 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: X-Spam-Status: No, score=-2.0 required=5.0 tests=ALL_TRUSTED, RATWARE_GECKO_BUILD Subject: Re: [Seqan-dev] Getting started with SeqAn 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 Dec 2011 11:44:09 -0000 Hi Robert, are you trying to generate Makefiles with CMake or which part of the Tutorial did you follow? What did you enter exactly to get the result from below? The output looks strange. Can you try to perform a new clean checkout: Could you try to enter the following on the shell? cd some-directory-where-you-want-to-do-the-checkout svn co http://svn.mi.fu-berlin.de/seqan/trunk/seqan seqan-trunk-NEW cd seqan-trunk-NEW mkdir -p build/Debug cd build/Debug cmake ../.. -DCMAKE_BUILD_TYPE=Debug This should work most probably. Otherwise, I would need the full output of the commands above. Bests, Manuel On 12/06/2011 10:06 AM, Robert Bakaric wrote: > Hello, > > I have a simple starter question. So I have downloaded the seqan and followed the instruction on "getting started": http://trac.seqan.de/wiki/Tutorial/GettingStarted , and that worked. but now i have tried to make some demos and i got the following message: > > > $ cmake2.8.6 . > > CMake Error at CMakeLists.txt:4 (seqan_setup_apps): > Unknown CMake command "seqan_setup_apps". > > > -- Configuring incomplete, errors occurred! > > > I'm probably missing something obvious but, don't see it.. > > My OS: Ubuntu 10.04 > g++ (Ubuntu 4.4.3-4ubuntu5) 4.4.3 > cmake version 2.8.6 > > > Thank you, > > Robert > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev From okko73313@gmail.com Tue Dec 06 14:22:29 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 <1RXuyZ-0000hx-AU>; Tue, 06 Dec 2011 14:22:27 +0100 Received: from mail-bw0-f54.google.com ([209.85.214.54]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RXuyZ-0006A9-7n>; Tue, 06 Dec 2011 14:22:27 +0100 Received: by bkat2 with SMTP id t2so10331644bka.13 for ; Tue, 06 Dec 2011 05:22:27 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=gamma; h=mime-version:reply-to:sender:date:x-google-sender-auth:message-id :subject:from:to:content-type; bh=Qe76lmkZuw6/huWPwfGDU9wXxyu/6CAvWBSIRETomIk=; b=nYJJDkK6YFwRdn99GXWuj5bqc8qV7KZ8s3sWaj5xBWXIP+fjrxWQHoGDoey4HbFFkX LEBuX2TXLSxIS5dKt4tpTCfDdjWczzRkQfJxlhy3746OgEoGd7q++YZPfM7efUF/IOgN mzeLQgoIEzjWrs9R/LXL4IVAr3tYw7UwylLFI= MIME-Version: 1.0 Received: by 10.180.7.164 with SMTP id k4mr17625079wia.52.1323177746934; Tue, 06 Dec 2011 05:22:26 -0800 (PST) Sender: okko73313@gmail.com Received: by 10.180.92.7 with HTTP; Tue, 6 Dec 2011 05:22:26 -0800 (PST) Date: Tue, 6 Dec 2011 14:22:26 +0100 X-Google-Sender-Auth: xxsouSTbAeyTTpqFD8VS_phQlFk Message-ID: From: Konstantin Okonechnikov To: seqan-dev@lists.fu-berlin.de Content-Type: multipart/alternative; boundary=f46d0442826a94a99504b36c53f0 X-Originating-IP: 209.85.214.54 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1323177747-000067B8-BDEDB209/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.003311, 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: X-Spam-Status: No, score=0.9 required=5.0 tests=DNS_FROM_RFC_ABUSE, HTML_20_30, HTML_MESSAGE,RCVD_BY_IP,SPF_HELO_PASS,SPF_PASS Subject: [Seqan-dev] minor mistake in seqan tutorial X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: k.okonechnikov@gmail.com, SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 06 Dec 2011 13:22:29 -0000 --f46d0442826a94a99504b36c53f0 Content-Type: text/plain; charset=ISO-8859-1 The "Getting Started" tutorial contains a minor mistake. Page: http://trac.seqan.de/wiki/Tutorial/GettingStarted#CreatingYourFirstApplication Code: >Within this sandbox, we can now create a new application using the code generator. ># cd ../.. ># ./util/bin/skel.py app my_app sandbox/my_sandbox The first command (cd ../..) is redundant since the working dir has already been changed earlier and application can not be created without an existing repository. Best regards, Konstantin --f46d0442826a94a99504b36c53f0 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable The "Getting Started" tutorial contains a minor mistake.

P= age:
http://trac.seqan.de/wiki/Tutorial/GettingStarted#C= reatingYourFirstApplication

Code:

>Within this sandbox, we can now create a new applicati= on using the code generator.
># cd ../..
># ./util/bin/skel.py = app my_app sandbox/my_sandbox

The first command=A0 (cd ../..) is red= undant since the working dir has already been changed earlier and applicati= on can not be created without an existing repository.

Best regards,
=A0=A0 Konstantin
--f46d0442826a94a99504b36c53f0-- From manuel.holtgrewe@fu-berlin.de Tue Dec 06 15:01:30 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 <1RXvaL-00026R-2W>; Tue, 06 Dec 2011 15:01:29 +0100 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 <1RXvaL-0007ME-0a>; Tue, 06 Dec 2011 15:01:29 +0100 Received: from ecoli.imp.fu-berlin.de ([160.45.111.133]) by inpost2.zedat.fu-berlin.de (Exim 4.69) with esmtpsa (envelope-from ) id <1RXvaK-0003VS-Uj>; Tue, 06 Dec 2011 15:01:29 +0100 Message-ID: <4EDE2014.8030501@fu-berlin.de> Date: Tue, 06 Dec 2011 15:00:52 +0100 From: Manuel Holtgrewe User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:8.0) Gecko/20111124 Thunderbird/8.0 MIME-Version: 1.0 To: "k.okonechnikov@gmail.com" , SeqAn Development References: In-Reply-To: Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Originating-IP: 160.45.111.133 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1323180089-000067B8-F2D952BA/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000142, 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: X-Spam-Status: No, score=-2.0 required=5.0 tests=ALL_TRUSTED, RATWARE_GECKO_BUILD Subject: Re: [Seqan-dev] minor mistake in seqan tutorial 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 Dec 2011 14:01:31 -0000 Thanks, I just corrected it. On 12/06/2011 02:22 PM, Konstantin Okonechnikov wrote: > The "Getting Started" tutorial contains a minor mistake. > > Page: > http://trac.seqan.de/wiki/Tutorial/GettingStarted#CreatingYourFirstApplication > > Code: > > >Within this sandbox, we can now create a new application using the > code generator. > ># cd ../.. > ># ./util/bin/skel.py app my_app sandbox/my_sandbox > > The first command (cd ../..) is redundant since the working dir has > already been changed earlier and application can not be created without > an existing repository. > > Best regards, > Konstantin From fheeger@mi.fu-berlin.de Thu Dec 15 14:40:48 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 <1RbBYE-0006wT-On>; Thu, 15 Dec 2011 14:40:46 +0100 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RbBYE-0007VQ-Mi>; Thu, 15 Dec 2011 14:40:46 +0100 Received: from bgbm6.bgbm.fu-berlin.de ([160.45.63.17] helo=[192.168.2.136]) by inpost2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtpsa (envelope-from ) id <1RbBYE-0008E6-JS>; Thu, 15 Dec 2011 14:40:46 +0100 From: Felix Heeger To: seqan-dev@lists.fu-berlin.de Content-Type: text/plain; charset="UTF-8" Date: Thu, 15 Dec 2011 14:40:42 +0100 Message-ID: <1323956442.11617.4.camel@IR0912.bgbm.fu-berlin.de> Mime-Version: 1.0 X-Mailer: Evolution 2.32.2 Content-Transfer-Encoding: 7bit X-Originating-IP: 160.45.63.17 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1323956446-000067B8-0C8D79EE/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 Gabun.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: [Seqan-dev] Error in parsing tutorial 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 Dec 2011 13:40:48 -0000 Hello, I think I found an error in the parsing tutorial. In the example code for the read* and skip* functions it says: > res = skipLine(buffer, reader); I think this has to be: > res = skipLine(reader); At least this is how it works for me. The comment function on the page is not working so I post this here. Cheers, felix From manuel.holtgrewe@fu-berlin.de Thu Dec 15 14:53:22 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 <1RbBkP-0007Ob-Iq>; Thu, 15 Dec 2011 14:53:21 +0100 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 <1RbBkP-0001wb-GX>; Thu, 15 Dec 2011 14:53:21 +0100 Received: from ecoli.imp.fu-berlin.de ([160.45.111.133]) by inpost2.zedat.fu-berlin.de (Exim 4.69) with esmtpsa (envelope-from ) id <1RbBkP-0000lg-EZ>; Thu, 15 Dec 2011 14:53:21 +0100 Message-ID: <4EE9FBA6.6000306@fu-berlin.de> Date: Thu, 15 Dec 2011 14:52:38 +0100 From: Manuel Holtgrewe User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:8.0) Gecko/20111124 Thunderbird/8.0 MIME-Version: 1.0 To: SeqAn Development References: <1323956442.11617.4.camel@IR0912.bgbm.fu-berlin.de> In-Reply-To: <1323956442.11617.4.camel@IR0912.bgbm.fu-berlin.de> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Originating-IP: 160.45.111.133 X-purgate: suspect X-purgate-type: suspect X-purgate-ID: 151147::1323957201-000067B8-84942845/3482853371-0/0-1 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 Algerien.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-1.8 required=5.0 tests=ALL_TRUSTED,FU_XPURGATE_SUSP Subject: Re: [Seqan-dev] Error in parsing tutorial 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 Dec 2011 13:53:22 -0000 Good catch, fixed both issues. On 12/15/2011 02:40 PM, Felix Heeger wrote: > Hello, > > I think I found an error in the parsing tutorial. > In the example code for the read* and skip* functions it says: >> res = skipLine(buffer, reader); > I think this has to be: >> res = skipLine(reader); > At least this is how it works for me. > > The comment function on the page is not working so I post this here. > > Cheers, > felix > > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev From merkle@in.tum.de Fri Dec 16 21:05:36 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 <1Rbe2B-0004xb-Uk>; Fri, 16 Dec 2011 21:05:36 +0100 Received: from mail-out1.informatik.tu-muenchen.de ([131.159.0.8]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Rbe2B-0007RA-Ri>; Fri, 16 Dec 2011 21:05:35 +0100 Received: from [129.187.209.132] (l132.tum.vpn.lrz.de [129.187.209.132]) (using TLSv1 with cipher AES256-SHA (256/256 bits)) (No client certificate requested) by mail.in.tum.de (Postfix) with ESMTP id A5F35EBF1 for ; Fri, 16 Dec 2011 21:05:34 +0100 (CET) Message-ID: <4EEBA47F.1060603@in.tum.de> Date: Fri, 16 Dec 2011 21:05:19 +0100 From: Johannes Merkle User-Agent: Mozilla/5.0 (Windows NT 6.1; WOW64; rv:8.0) Gecko/20111105 Thunderbird/8.0 MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de Content-Type: multipart/alternative; boundary="------------030502000704090202030705" X-Originating-IP: 131.159.0.8 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1324065935-000067B8-4224A5D0/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.300136, 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: X-Spam-Status: No, score=0.1 required=5.0 tests=HTML_40_50,HTML_MESSAGE Subject: [Seqan-dev] Reading very long sequences from file 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: Fri, 16 Dec 2011 20:05:36 -0000 This is a multi-part message in MIME format. --------------030502000704090202030705 Content-Type: text/plain; charset=ISO-8859-15; format=flowed Content-Transfer-Encoding: 7bit Hello, I'm trying to read a sequence from a textfile has a size of around 3gigabytes based on the tutorial to import millions of sequences. For files bigger than around 1.5gig the program of the tutorial immediately stops because open(multiSeqFile.concat, argv[1], OPEN_RDONLY) returns false. For file(s) (since i only tested it with one file) bigger than around 700mb the program crashs on an invalid null pointer after a while. What are the limitations here? I'm running this on a win7 64 machine with 4gig of ram. The program is compiled in visual studio 2010 Is there a better way to do this? Since i'm not trying to read multiple sequences but only one that is very large. Thanks, Johannes --------------030502000704090202030705 Content-Type: text/html; charset=ISO-8859-15 Content-Transfer-Encoding: 8bit Hello,

I'm trying to read a sequence from a textfile has a size of around 3gigabytes based on the tutorial to import millions of sequences.

For files bigger than around 1.5gig the program of the tutorial immediately stops because open(multiSeqFile.concat, argv[1], OPEN_RDONLY)  returns false.

For file(s) (since i only tested it with one file) bigger than around 700mb the program crashs on an invalid null pointer after a while.

What are the limitations here? I'm running this on a win7 64 machine with 4gig of ram. The program is compiled in visual studio 2010

Is there a better way to do this? Since i'm not trying to read multiple sequences but only one that is very large.

Thanks,
Johannes
--------------030502000704090202030705-- From manuel.holtgrewe@fu-berlin.de Mon Dec 19 17:11:15 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 <1Rcfo1-0008Rp-A1>; Mon, 19 Dec 2011 17:11:13 +0100 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 <1Rcfo1-0002VO-80>; Mon, 19 Dec 2011 17:11:13 +0100 Received: from ecoli.imp.fu-berlin.de ([160.45.111.133]) by inpost2.zedat.fu-berlin.de (Exim 4.69) with esmtpsa (envelope-from ) id <1Rcfo1-0002kr-5r>; Mon, 19 Dec 2011 17:11:13 +0100 Message-ID: <4EEF61F3.6010502@fu-berlin.de> Date: Mon, 19 Dec 2011 17:10:27 +0100 From: Manuel Holtgrewe User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:8.0) Gecko/20111124 Thunderbird/8.0 MIME-Version: 1.0 To: SeqAn Development References: <4EEBA47F.1060603@in.tum.de> In-Reply-To: <4EEBA47F.1060603@in.tum.de> Content-Type: text/plain; charset=ISO-8859-15; format=flowed Content-Transfer-Encoding: 7bit X-Originating-IP: 160.45.111.133 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1324311073-000067B8-2BDC3E37/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.001143, 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 very long sequences from file 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, 19 Dec 2011 16:11:15 -0000 Short answer: Try using the "Visual Studio 10 Win64" generator, your problem appears to be that you are doing 32 bit builds such that your application can only use 2 GB of main memory. This should resolve the problems described below. Note that SeqAn rounds up the allocated memory when using Generous() allocation (the default) such that the problem might occur earlier than you expect. I reproduced your error with the 1.5 gig file on Windows 7 with Visual Studio 2010, using a 2GB file in a 32 bit build: I tracked the error down to a failing MapViewOfFile() call. This is a Windows API call, so you might want to look up the limitations of this function. The assignSeq() function itself is written such that only constant memory plus the resulting string is required for reading files. I also reproduced your other problem with the a 800 MB file. Here, the internal aligned malloc call returns NULL which is not handled by SeqAn. I already added a ticket for this here https://trac.seqan.de/ticket/925 Note that this ticket only asks for notifying the user that a malloc error happened but it would not enable you to make the function work in your configuration. On 12/16/2011 09:05 PM, Johannes Merkle wrote: > Hello, > > I'm trying to read a sequence from a textfile has a size of around > 3gigabytes based on the tutorial to import millions of sequences. > > For files bigger than around 1.5gig the program of the tutorial > immediately stops because open(multiSeqFile.concat, argv[1], > OPEN_RDONLY) returns false. > > For file(s) (since i only tested it with one file) bigger than around > 700mb the program crashs on an invalid null pointer after a while. > > What are the limitations here? I'm running this on a win7 64 machine > with 4gig of ram. The program is compiled in visual studio 2010 > > Is there a better way to do this? Since i'm not trying to read multiple > sequences but only one that is very large. > > Thanks, > Johannes > From s9nikoch@stud.uni-saarland.de Wed Dec 21 15:32:08 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 <1RdNDD-0000bs-LU>; Wed, 21 Dec 2011 15:32:08 +0100 Received: from theia.rz.uni-saarland.de ([134.96.7.31]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RdNDD-0001D4-I2>; Wed, 21 Dec 2011 15:32:07 +0100 Received: from webmail.uni-saarland.de (webmail.uni-saarland.de [134.96.1.53]) by theia.rz.uni-saarland.de (8.14.1/8.14.0) with ESMTP id pBLEW6sF003504 for ; Wed, 21 Dec 2011 15:32:06 +0100 Received: from dslb-084-058-207-159.pools.arcor-ip.net (dslb-084-058-207-159.pools.arcor-ip.net [84.58.207.159]) by webmail.uni-saarland.de (Horde Framework) with HTTP; Wed, 21 Dec 2011 15:32:05 +0100 Message-ID: <20111221153205.151140lk0256qspx@webmail.uni-saarland.de> Date: Wed, 21 Dec 2011 15:32:05 +0100 From: Nikola Koch To: seqan-dev@lists.fu-berlin.de MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Content-Disposition: inline Content-Transfer-Encoding: 7bit User-Agent: Internet Messaging Program (IMP) H3 (4.3.9) X-Greylist: Sender IP whitelisted, not delayed by milter-greylist-3.0 (theia.rz.uni-saarland.de [134.96.7.31]); Wed, 21 Dec 2011 15:32:06 +0100 (CET) X-AntiVirus: checked by AntiVir MailGate (version: 2.1.2-14; AVE: 7.9.8.8; VDF: 7.11.19.211; host: AntiVir1) X-Originating-IP: 134.96.7.31 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1324477927-000067B8-34C0451E/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.072736, 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=-0.0 required=5.0 tests=SPF_HELO_PASS Subject: [Seqan-dev] Gapped Sequence Itertor seems to trim Gaps at Beginning/Ending of a Row 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: Wed, 21 Dec 2011 14:32:08 -0000 Hi, I'm using Seqan for my Bachelor's thesis, which consists of writing an alignment window for BALL. Since I need to have pointers from the sequences back to the corresponding residues, I have to create my own sequence and alignment representations that link back to their origins. For computing the actual alignment, I want to use Seqan. So I have to push my representations into the Seqan structures and after computing the alignment, retrieve the alignment from the Seqan structures and push it into my own structures. The Seqan structures I use, are the same as described in your tutorial (I'm not using an alignment graph) And here comes my problem: When retrieving the Alignment from your structures I use two iterators to iterate over the gapped rows (and columns). But when there are gaps at the beginning (or the end) of a row, the iterator seems to just ignore them and starts with the character right after the gap (or ends with the last character in front of the gap). For example: ---AL-GI-- then becomes AL-GI. The length of such a gapped row seems to also be the length of the row without starting/ending gaps. But when using std::cout with the whole alignment, all gaps are, where they should be. I consulted the Seqan documentation but without result. So is there a possibility to externally gain access to the gaps at the beginning/end of each row? Or is there a better way to retrieve the alignment than iterating over all rows? Thanks, Nikola From manuel.holtgrewe@fu-berlin.de Wed Dec 21 17:03:36 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 <1RdOdi-0003KU-2B>; Wed, 21 Dec 2011 17:03:34 +0100 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 <1RdOdh-000475-Vx>; Wed, 21 Dec 2011 17:03:34 +0100 Received: from ecoli.imp.fu-berlin.de ([160.45.111.133]) by inpost2.zedat.fu-berlin.de (Exim 4.69) with esmtpsa (envelope-from ) id <1RdOdh-0003mL-Tn>; Wed, 21 Dec 2011 17:03:33 +0100 Message-ID: <4EF20326.6070404@fu-berlin.de> Date: Wed, 21 Dec 2011 17:02:46 +0100 From: Manuel Holtgrewe User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:8.0) Gecko/20111124 Thunderbird/8.0 MIME-Version: 1.0 To: SeqAn Development References: <20111221153205.151140lk0256qspx@webmail.uni-saarland.de> In-Reply-To: <20111221153205.151140lk0256qspx@webmail.uni-saarland.de> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Originating-IP: 160.45.111.133 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1324483414-000067B8-A9606F3F/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000950, 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: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: Re: [Seqan-dev] Gapped Sequence Itertor seems to trim Gaps at Beginning/Ending of a Row 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: Wed, 21 Dec 2011 16:03:36 -0000 Hi Nikolai, this weakness of the Gaps data structure is known to us and on our "to be fixed" list. Off the top of my head, I would look into the alignment printing function here: http://trac.seqan.de/browser/trunk/seqan/core/include/seqan/align/align_base.h#L468 It appears that you have to use the iter() function together with length() but not the begin() and end functions. :( The solution to the Task 1 in alignments uses the iter() function as well: http://trac.seqan.de/wiki/Tutorial/Alignments/AssignmentPairwiseGlobalAlignment1 HTH Manuel On 12/21/2011 03:32 PM, Nikola Koch wrote: > Hi, > I'm using Seqan for my Bachelor's thesis, which consists of writing an > alignment window for BALL. > Since I need to have pointers from the sequences back to the > corresponding residues, I have to create my own sequence and alignment > representations that link back to their origins. > For computing the actual alignment, I want to use Seqan. > So I have to push my representations into the Seqan structures and > after computing the alignment, retrieve the alignment from the Seqan > structures and push it into my own structures. The Seqan structures I > use, are the same as described in your tutorial (I'm not using an > alignment graph) > And here comes my problem: > When retrieving the Alignment from your structures I use two iterators > to iterate over the gapped rows (and columns). > But when there are gaps at the beginning (or the end) of a row, the > iterator seems to just ignore them and starts with the character right > after the gap (or ends with the last character in front of the gap). > For example: ---AL-GI-- then becomes AL-GI. > > The length of such a gapped row seems to also be the length of the row > without starting/ending gaps. > > But when using std::cout with the whole alignment, all gaps are, where > they should be. > > I consulted the Seqan documentation but without result. > > So is there a possibility to externally gain access to the gaps at the > beginning/end of each row? > Or is there a better way to retrieve the alignment than iterating over > all rows? > > Thanks, > Nikola > > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev From fheeger@mi.fu-berlin.de Wed Dec 21 17:15:51 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 <1RdOpa-0003k0-PK>; Wed, 21 Dec 2011 17:15:50 +0100 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RdOpa-0006hX-NH>; Wed, 21 Dec 2011 17:15:50 +0100 Received: from bgbm6.bgbm.fu-berlin.de ([160.45.63.17] helo=[192.168.2.136]) by inpost2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtpsa (envelope-from ) id <1RdOpa-0004af-L0>; Wed, 21 Dec 2011 17:15:50 +0100 From: Felix Heeger To: seqan-dev Content-Type: text/plain; charset="UTF-8" Date: Wed, 21 Dec 2011 17:15:50 +0100 Message-ID: <1324484150.19199.29.camel@IR0912.bgbm.fu-berlin.de> Mime-Version: 1.0 X-Mailer: Evolution 2.32.2 Content-Transfer-Encoding: 7bit X-Originating-IP: 160.45.63.17 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1324484150-000067B8-4373252A/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=-2.8 required=5.0 tests=ALL_TRUSTED Subject: [Seqan-dev] CheckStreamFormat for FastQ 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: Wed, 21 Dec 2011 16:15:51 -0000 Hi, I have to different functions I want to call depending on the fact if a input file is fasta or fastq format. My approach to this is: > RecordReader > reader(inFile); > if (checkStreamFormat(reader, Fasta())) > { > std::cerr << "Input file format is fasta." << std::endl; > [call function for fasta] > } > else if (checkStreamFormat(reader, Fastq())) > { > std::cerr << "Input file format is fastq." << std::endl; > [call function for fastq] > } > else > { > std::cerr << "ERORR: Input file format is not fasta or fastq." << std::endl; > return -1; > } This works fine for fasta. However my fastq file is not recognized. I looked into the code for checkStreamFormat a bit and the file is not recognized because the iterator in the readRecord function reaches atEnd before the quality meta data for the 35th record is finished (l. 392). This happens with two different fastq files. So my theory is the following: In the checkStreamFormat function LimitRecordReaderInScope is used. The documentation states that this prevents the stream from "rebuffering". This probably prevents the reader from finishing to read the complete record and the recognition of the file fails. I hope I could make myself clear. I can also provide my code and a sample fastq file if it would be helpful. Cheers, felix From manuel.holtgrewe@fu-berlin.de Wed Dec 21 18:32:04 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 <1RdQ1K-00065s-Pl>; Wed, 21 Dec 2011 18:32:02 +0100 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 <1RdQ1K-0002d5-NM>; Wed, 21 Dec 2011 18:32:02 +0100 Received: from ecoli.imp.fu-berlin.de ([160.45.111.133]) by inpost2.zedat.fu-berlin.de (Exim 4.69) with esmtpsa (envelope-from ) id <1RdQ1K-0000VD-LI>; Wed, 21 Dec 2011 18:32:02 +0100 Message-ID: <4EF217E3.1000605@fu-berlin.de> Date: Wed, 21 Dec 2011 18:31:15 +0100 From: Manuel Holtgrewe User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:8.0) Gecko/20111124 Thunderbird/8.0 MIME-Version: 1.0 To: SeqAn Development References: <1324484150.19199.29.camel@IR0912.bgbm.fu-berlin.de> In-Reply-To: <1324484150.19199.29.camel@IR0912.bgbm.fu-berlin.de> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Originating-IP: 160.45.111.133 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1324488722-000067B8-D2AE10F5/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000001, 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] CheckStreamFormat for FastQ 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: Wed, 21 Dec 2011 17:32:05 -0000 Felix, The documentation of checkStreamFormat() was misleading. I fixed it in [10948]. http://docs.seqan.de/seqan/dev2/?i=Function.checkStreamFormat (The documentation is regenerated every hour, so you might wait for a bit to see it). The following is a simple example program I compiled and tested. Please write another email, if the problem persists. HTH, Manuel #include #include #include #include int main(int argc, char ** argv) { using namespace seqan; if (argc != 2) return 1; std::fstream in(argv[1]); RecordReader > reader(in); AutoSeqStreamFormat tagSelector; bool b = checkStreamFormat(reader, tagSelector); if (!b) { std::cerr << "Could not detect file format!" << std::endl; return 1; } // b is true if any format was detected successfully. if (tagSelector.tagId == 1) std::cerr << "Detected FASTA." << std::endl; else if (tagSelector.tagId == 2) std::cerr << "Detected FASTQ." << std::endl; else std::cerr << "Unknown file format!" << std::endl; return 0; } On 12/21/2011 05:15 PM, Felix Heeger wrote: > Hi, > > I have to different functions I want to call depending on the fact if a > input file is fasta or fastq format. > > My approach to this is: > >> RecordReader > reader(inFile); >> if (checkStreamFormat(reader, Fasta())) >> { >> std::cerr<< "Input file format is fasta."<< std::endl; >> [call function for fasta] >> } >> else if (checkStreamFormat(reader, Fastq())) >> { >> std::cerr<< "Input file format is fastq."<< std::endl; >> [call function for fastq] >> } >> else >> { >> std::cerr<< "ERORR: Input file format is not fasta or fastq."<< std::endl; >> return -1; >> } > > This works fine for fasta. However my fastq file is not recognized. > I looked into the code for checkStreamFormat a bit and the file is not > recognized because the iterator in the readRecord function reaches > atEnd before the quality meta data for the 35th record is finished (l. 392). > This happens with two different fastq files. > > So my theory is the following: > In the checkStreamFormat function LimitRecordReaderInScope > is used. The documentation states that this prevents the stream from > "rebuffering". This probably prevents the reader from finishing to read > the complete record and the recognition of the file fails. > > I hope I could make myself clear. I can also provide my code and a sample > fastq file if it would be helpful. > > Cheers, > felix > > > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev