From s.henderson@ucl.ac.uk Thu May 09 13:32:02 2013 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UaP4r-003XeW-75>; Thu, 09 May 2013 13:32:01 +0200 Received: from mail-db8lp0185.outbound.messaging.microsoft.com ([213.199.154.185] helo=db8outboundpool.messaging.microsoft.com) by relay1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UaP4r-003DRC-3W>; Thu, 09 May 2013 13:32:01 +0200 Received: from mail215-db8-R.bigfish.com (10.174.8.238) by DB8EHSOBE006.bigfish.com (10.174.4.69) with Microsoft SMTP Server id 14.1.225.23; Thu, 9 May 2013 11:31:58 +0000 Received: from mail215-db8 (localhost [127.0.0.1]) by mail215-db8-R.bigfish.com (Postfix) with ESMTP id 0A657420474 for ; Thu, 9 May 2013 11:31:58 +0000 (UTC) X-Forefront-Antispam-Report: CIP:157.56.250.117; KIP:(null); UIP:(null); IPV:NLI; H:AMXPRD0111HT003.eurprd01.prod.exchangelabs.com; RD:none; EFVD:NLI X-SpamScore: 0 X-BigFish: PS0(z569dhzzz1f42h1ee6h1de0h1d18h1fdah1202h1e76h1d1ah1d2ah1fc6hzzz2dh2a8h668h839h944hd25hf0ah1220h1288h12a5h12a9h12bdh137ah13b6h1441h1504h1537h153bh15d0h162dh1631h1758h18e1h1946h19b5h19ceh1ad9h1b0ah1d07h1d0ch1d2eh1d3fh1155h) Received: from mail215-db8 (localhost.localdomain [127.0.0.1]) by mail215-db8 (MessageSwitch) id 136809911656344_11347; Thu, 9 May 2013 11:31:56 +0000 (UTC) Received: from DB8EHSMHS013.bigfish.com (unknown [10.174.8.237]) by mail215-db8.bigfish.com (Postfix) with ESMTP id F144E300044 for ; Thu, 9 May 2013 11:31:55 +0000 (UTC) Received: from AMXPRD0111HT003.eurprd01.prod.exchangelabs.com (157.56.250.117) by DB8EHSMHS013.bigfish.com (10.174.4.23) with Microsoft SMTP Server (TLS) id 14.1.225.23; Thu, 9 May 2013 11:31:55 +0000 Received: from AMXPRD0111MB472.eurprd01.prod.exchangelabs.com ([169.254.10.48]) by AMXPRD0111HT003.eurprd01.prod.exchangelabs.com ([10.242.12.164]) with mapi id 14.16.0305.001; Thu, 9 May 2013 11:31:55 +0000 From: "Henderson, Stephen" To: "seqan-dev@lists.fu-berlin.de" Thread-Topic: countKmers Thread-Index: AQHOTKjOo2Tp9tkic0K3rNsZ9blAbw== Date: Thu, 9 May 2013 11:31:55 +0000 Message-ID: <98456EB61783264C9A843890618267F84FEE9EDD@AMXPRD0111MB472.eurprd01.prod.exchangelabs.com> Accept-Language: en-GB, en-US Content-Language: en-GB X-MS-Has-Attach: X-MS-TNEF-Correlator: x-ucllive-sclrule: HASRUN Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-OriginatorOrg: ucl.ac.uk X-Originating-IP: 213.199.154.185 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1368099121-00000A3F-7950B748/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000107, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=0.0 required=5.0 tests=RCVD_IN_DNSWL_NONE X-Spam-Checker-Version: SpamAssassin 3.3.3-zedat9255cc3 on Benin.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] countKmers X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 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, 09 May 2013 11:32:02 -0000 Hello=0A= =0A= I think I'm confused by what is the current/trunk/development versions? I h= ave downloaded 1.4 which I think is the trunk? I had to change a few keywor= ds (Mapped -> StringReader) to make my old code work. But I do not see the = useful countKmers function that I downloaded the latest version for:=0A= =0A= countKmers(kmerCounts, sequence, k)=0A= countKmers(kmerCounts, backgroundFrequencies, sequence, k)=0A= countKmers(kmerCounts, bgModel, sequence, k)=0A= =0A= This should be in align_free and align_free.h ?=0A= =0A= Is this in a dev version somewhere?=0A= =0A= Thanks=0A= Stephen Henderson=0A= UCL Cancer Institute = From weese@campus.fu-berlin.de Thu May 09 14:29:15 2013 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UaPyE-003gmD-JV>; Thu, 09 May 2013 14:29:14 +0200 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UaPyE-001Zgi-Hn>; Thu, 09 May 2013 14:29:14 +0200 Received: from cas2.campus.fu-berlin.de ([130.133.170.202]) by relay2.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UaPyE-0022RV-74>; Thu, 09 May 2013 14:29:14 +0200 Received: from EX02A.campus.fu-berlin.de ([130.133.170.132]) by CAS2.campus.fu-berlin.de ([130.133.170.202]) with mapi id 14.03.0123.003; Thu, 9 May 2013 14:29:08 +0200 From: "Weese, David" To: SeqAn Development Thread-Topic: [Seqan-dev] countKmers Thread-Index: AQHOTKjOo2Tp9tkic0K3rNsZ9blAb5j8pr8A Message-ID: <14304786-2C4F-4EF5-B7AC-4E49E0B269FD@fu-berlin.de> References: <98456EB61783264C9A843890618267F84FEE9EDD@AMXPRD0111MB472.eurprd01.prod.exchangelabs.com> In-Reply-To: <98456EB61783264C9A843890618267F84FEE9EDD@AMXPRD0111MB472.eurprd01.prod.exchangelabs.com> Accept-Language: de-DE, en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: text/plain; charset="iso-8859-1" Content-ID: Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 Date: Thu, 09 May 2013 14:29:06 +0200 X-Original-Date: Thu, 9 May 2013 12:29:06 +0000 X-Originating-IP: 130.133.170.202 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1368102554-00000A3F-1C7D2657/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=-50.0 required=5.0 tests=ALL_TRUSTED X-Spam-Checker-Version: SpamAssassin 3.3.3-zedat9255cc3 on Algerien.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] countKmers X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 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, 09 May 2013 12:29:15 -0000 Hi Stephen, currently there is not much of a difference between the trunk and the 1.4 r= elease, which we tagged from the trunk just a couple of days ago. In the re= lease we simply merged the trunk folders core/include and extras/include in= to one include folder. You'll get the countKmers functions if you include the alignment_free modu= le by #include . You can find the sources in (extra= s/)include/seqan/alignment_free/kmer_functions.h=20 HTH, David -- David Weese weese@inf.fu-berlin.de Freie Universit=E4t Berlin http://www.inf.fu-berlin.de/ Institut f=FCr Informatik Phone: +49 30 838 75137 Takustra=DFe 9 Algorithmic Bioinformatics 14195 Berlin Room 020=20 Am 09.05.2013 um 13:31 schrieb "Henderson, Stephen" = : > Hello >=20 > I think I'm confused by what is the current/trunk/development versions? I= have downloaded 1.4 which I think is the trunk? I had to change a few keyw= ords (Mapped -> StringReader) to make my old code work. But I do not see th= e useful countKmers function that I downloaded the latest version for: >=20 > countKmers(kmerCounts, sequence, k) > countKmers(kmerCounts, backgroundFrequencies, sequence, k) > countKmers(kmerCounts, bgModel, sequence, k) >=20 > This should be in align_free and align_free.h ? >=20 > Is this in a dev version somewhere? >=20 > Thanks > Stephen Henderson > UCL Cancer Institute=20 > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev From studium@mindcode.de Fri May 10 13:20:42 2013 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UalNQ-001Yxp-Eg>; Fri, 10 May 2013 13:20:40 +0200 Received: from mail.mindcode.de ([82.211.56.236]) by relay1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UalNQ-002Gyf-AO>; Fri, 10 May 2013 13:20:40 +0200 Received: from mail.mindcode.de (mail.mindcode.de [82.211.56.236]) (Authenticated sender: studium@mindcode.de) by mail.mindcode.de (Postfix) with ESMTPA id 08958A28E5 for ; Fri, 10 May 2013 13:20:37 +0200 (CEST) MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="=_05b76cd0f4ca5e5cd125934620cc8a66" Date: Fri, 10 May 2013 13:20:36 +0200 From: Matthias Loose To: seqan-dev@lists.fu-berlin.de Message-ID: <4f076d3f296b8021f0620cbeb97c09e9@mindcode.de> X-Sender: studium@mindcode.de User-Agent: Roundcube Webmail/0.8.4 X-Originating-IP: 82.211.56.236 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1368184840-00000A3F-F29246EE/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.125383, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=0.0 required=5.0 tests=none X-Spam-Checker-Version: SpamAssassin 3.3.3-zedat9255cc3 on Gabun.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] Problem using SeqAn with VS11 X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 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, 10 May 2013 11:20:42 -0000 --=_05b76cd0f4ca5e5cd125934620cc8a66 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; format=flowed Hello, I wanted to use SeqAn without the provided build system for just a couple functions in a Project. Im using Visual Studio 11 right now and according to this site: http://trac.seqan.de/wiki/BuildManual/IntegrationWithYourOwnBuildSystem all I need to do is include the seqan/include directory which I have done to a new Project. To test it Im using this file: #include #include // CharString, ... #include // to stream a CharString into cout int main(int, char const **) { std::cout << "Hello World!" << std::endl; seqan::CharString mySeqanString = "Hello SeqAn!"; std::cout << mySeqanString << std::endl; return 1; } Unfortunatly I get a lot of errors on build time. I attached the output to this message. If I build the "first_app" using the provided build system it builds fine, but for now Id rather juts use Seqan in my already started project and the prospect of just adding seqan to my includes seemes really nice. Any help would be appreciated. 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(MessageSwitch) id 1368200745991452_7177; Fri, 10 May 2013 15:45:45 +0000 (UTC) Received: from CO1EHSMHS011.bigfish.com (unknown [10.243.78.233]) by mail140-co1.bigfish.com (Postfix) with ESMTP id F05F19A0A9C for ; Fri, 10 May 2013 15:45:45 +0000 (UTC) Received: from AMXPRD0111HT002.eurprd01.prod.exchangelabs.com (157.56.250.117) by CO1EHSMHS011.bigfish.com (10.243.66.21) with Microsoft SMTP Server (TLS) id 14.1.225.23; Fri, 10 May 2013 15:45:44 +0000 Received: from AMXPRD0111MB472.eurprd01.prod.exchangelabs.com ([169.254.10.48]) by AMXPRD0111HT002.eurprd01.prod.exchangelabs.com ([10.242.12.163]) with mapi id 14.16.0305.001; Fri, 10 May 2013 15:45:42 +0000 From: "Henderson, Stephen" To: "seqan-dev@lists.fu-berlin.de" Thread-Topic: seqan-dev Digest, Vol 44, Issue 1 Thread-Index: AQHOTWXScbqWmJOorEW+UG5NrQIvJ5j+iJ5s Date: Fri, 10 May 2013 15:45:42 +0000 Message-ID: <98456EB61783264C9A843890618267F84FEEB484@AMXPRD0111MB472.eurprd01.prod.exchangelabs.com> References: In-Reply-To: Accept-Language: en-GB, en-US Content-Language: en-GB X-MS-Has-Attach: X-MS-TNEF-Correlator: x-ucllive-sclrule: HASRUN Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-OriginatorOrg: ucl.ac.uk X-Originating-IP: 216.32.180.184 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1368200752-00000A3F-7E352F17/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=-0.7 required=5.0 tests=RCVD_IN_DNSWL_LOW X-Spam-Checker-Version: SpamAssassin 3.3.3-zedat9255cc3 on Burundi.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] seqan-dev Digest, Vol 44, Issue 1 X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 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, 10 May 2013 15:45:53 -0000 Hi David=0A= =0A= Thanks. That is understood, I found the .h files where you said and it work= s well. =0A= =0A= I have other problems... but it's Friday so I think I'll struggle on and no= t bother you for a bit ;0=0A= =0A= Stephen=0A= =0A= =0A= =0A= ------------------------------=0A= Date: Thu, 09 May 2013 14:29:06 +0200=0A= From: "Weese, David" =0A= To: SeqAn Development =0A= Subject: Re: [Seqan-dev] countKmers=0A= Message-ID: <14304786-2C4F-4EF5-B7AC-4E49E0B269FD@fu-berlin.de>=0A= Content-Type: text/plain; charset=3D"iso-8859-1"=0A= =0A= Hi Stephen,=0A= =0A= currently there is not much of a difference between the trunk and the 1.4 r= elease, which we tagged from the trunk just a couple of days ago. In the re= lease we simply merged the trunk folders core/include and extras/include in= to one include folder.=0A= You'll get the countKmers functions if you include the alignment_free modu= le by #include . You can find the sources in (extra= s/)include/seqan/alignment_free/kmer_functions.h=0A= =0A= HTH,=0A= David=0A= =0A= --=0A= David Weese weese@inf.fu-berlin.de=0A= Freie Universit?t Berlin http://www.inf.fu-berlin.de/=0A= Institut f?r Informatik Phone: +49 30 838 75137=0A= Takustra?e 9 Algorithmic Bioinformatics= =0A= 14195 Berlin Room 020=0A= =0A= From weese@campus.fu-berlin.de Fri May 10 19:46:42 2013 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UarOy-002KEy-UJ>; Fri, 10 May 2013 19:46:41 +0200 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UarOy-000Rx2-SK>; Fri, 10 May 2013 19:46:40 +0200 Received: from cas1.campus.fu-berlin.de ([130.133.170.201]) by relay2.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UarOy-000s1Y-Gk>; Fri, 10 May 2013 19:46:40 +0200 Received: from EX02A.campus.fu-berlin.de ([130.133.170.132]) by CAS1.campus.fu-berlin.de ([130.133.170.201]) with mapi id 14.03.0123.003; Fri, 10 May 2013 19:46:39 +0200 From: "Weese, David" To: SeqAn Development Thread-Topic: [Seqan-dev] Problem using SeqAn with VS11 Thread-Index: AQHOTXCEPdE9+TzLXk2wmVskWYNeLZj+scTw Message-ID: <7F0C5BB7-35EC-40E7-B670-ADF787DF18E5@campus.fu-berlin.de> References: <4f076d3f296b8021f0620cbeb97c09e9@mindcode.de> In-Reply-To: <4f076d3f296b8021f0620cbeb97c09e9@mindcode.de> Accept-Language: de-DE, en-US Content-Language: de-DE X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: multipart/alternative; boundary="_000_7F0C5BB735EC40E7B670ADF787DF18E5campusfuberlinde_" MIME-Version: 1.0 Date: Fri, 10 May 2013 19:46:38 +0200 X-Original-Date: Fri, 10 May 2013 17:46:38 +0000 X-Originating-IP: 130.133.170.201 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1368208000-00000A3F-33CA438E/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.008907, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=-49.7 required=5.0 tests=ALL_TRUSTED, HTML_FONT_FACE_BAD,HTML_MESSAGE X-Spam-Checker-Version: SpamAssassin 3.3.3-zedat9255cc3 on Dschibuti.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] Problem using SeqAn with VS11 X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 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, 10 May 2013 17:46:42 -0000 --_000_7F0C5BB735EC40E7B670ADF787DF18E5campusfuberlinde_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Hi Matthias, It seems that you missed to set the recommended compiler flags. See: http://trac.seqan.de/wiki/BuildManual/IntegrationWithYourOwnBuildSystem#Com= pilerFlags At least you should go to warning level 2 and add the definition _CRT_SECUR= E_NO_WARNINGS. Cheers, David Von meinem iPad gesendet Am 10.05.2013 um 13:21 schrieb "Matthias Loose" >: Hello, I wanted to use SeqAn without the provided build system for just a couple f= unctions in a Project. Im using Visual Studio 11 right now and according to= this site: http://trac.seqan.de/wiki/BuildManual/IntegrationWithYourOwnBuildSystem all I need to do is include the seqan/include directory which I have done t= o a new Project. To test it Im using this file: #include #include // CharString, ... #include // to stream a CharString into cout int main(int, char const **) { std::cout << "Hello World!" << std::endl; seqan::CharString mySeqanString =3D "Hello SeqAn!"; std::cout << mySeqanString << std::endl; return 1; } Unfortunatly I get a lot of errors on build time. I attached the output to = this message. If I build the "first_app" using the provided build system it= builds fine, but for now Id rather juts use Seqan in my already started pr= oject and the prospect of just adding seqan to my includes seemes really ni= ce. Any help would be appreciated. Matthias Loose _______________________________________________ seqan-dev mailing list seqan-dev@lists.fu-berlin.de https://lists.fu-berlin.de/listinfo/seqan-dev --_000_7F0C5BB735EC40E7B670ADF787DF18E5campusfuberlinde_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable
Hi Matthias,

It seems that you missed to= set the recommended compiler flags. See:

At least you should go to warning level 2 and add the definition _CRT_SEC= URE_NO_WARNINGS.

Cheer= s,
David=

Von meinem iPad gesendet

Am 10.05.2013 um 13:21 schrieb "Matthias Loose" <studium@mindcode.de>:

Hello,

I wanted to use SeqAn without the provided build system for just a co= uple functions in a Project. Im using Visual Studio 11 right now and accord= ing to this site:

http://trac.seqan.de/wiki/BuildManual/IntegrationWithYourOwn= BuildSystem

all I need to do is include the seqan/include directory which I have = done to a new Project. To test it Im using this file:


#include <iostream>
#include <seqan/sequence.h>  // CharString, ...
#include <seqan/file.h>      // to str= eam a CharString into cout

int main(int, char const **)
{
std::cout << "Hello World!" << std::endl;
seqan::CharString mySeqanString =3D "Hello SeqAn!";<= br> std::cout << mySeqanString << std::endl;
return 1;
}

Unfortunatly I get a lot of errors on build time. I attached the outp= ut to this message. If I build the "first_app" using the provided= build system it builds fine, but for now Id rather juts use Seqan in my al= ready started project and the prospect of just adding seqan to my includes seemes really nice.

Any help would be appreciated.


Matthias Loose
<seqan_error.txt>
_______________________________________________
seqan-dev mailing list
seqan-dev@lists.fu-be= rlin.de
https://lis= ts.fu-berlin.de/listinfo/seqan-dev
--_000_7F0C5BB735EC40E7B670ADF787DF18E5campusfuberlinde_-- From weese@campus.fu-berlin.de Fri May 10 19:58:41 2013 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UaraZ-002M3W-R1>; Fri, 10 May 2013 19:58:39 +0200 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UaraZ-000VWf-P8>; Fri, 10 May 2013 19:58:39 +0200 Received: from cas1.campus.fu-berlin.de ([130.133.170.201]) by relay2.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UaraZ-000tRp-Di>; Fri, 10 May 2013 19:58:39 +0200 Received: from EX02A.campus.fu-berlin.de ([130.133.170.132]) by CAS1.campus.fu-berlin.de ([130.133.170.201]) with mapi id 14.03.0123.003; Fri, 10 May 2013 19:58:38 +0200 From: "Weese, David" To: SeqAn Development Thread-Topic: [Seqan-dev] Problem using SeqAn with VS11 Thread-Index: AQHOTXCEPdE9+TzLXk2wmVskWYNeLZj+tR1p Message-ID: References: <4f076d3f296b8021f0620cbeb97c09e9@mindcode.de> In-Reply-To: <4f076d3f296b8021f0620cbeb97c09e9@mindcode.de> Accept-Language: de-DE, en-US Content-Language: de-DE X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: multipart/alternative; boundary="_000_C62692B903AA4DDE9D98D056529C253Ccampusfuberlinde_" MIME-Version: 1.0 Date: Fri, 10 May 2013 19:58:37 +0200 X-Original-Date: Fri, 10 May 2013 17:58:37 +0000 X-Originating-IP: 130.133.170.201 X-ZEDAT-Hint: A X-purgate: suspect X-purgate-type: suspect X-purgate-ID: 151147::1368208719-00000A3F-7497B6AC/0-10660300156/0-2 X-Bogosity: Ham, tests=bogofilter, spamicity=0.025888, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=-49.0 required=5.0 tests=ALL_TRUSTED, FU_XPURGATE_SUSP, HTML_MESSAGE X-Spam-Checker-Version: SpamAssassin 3.3.3-zedat9255cc3 on Botsuana.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] Problem using SeqAn with VS11 X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 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, 10 May 2013 17:58:41 -0000 --_000_C62692B903AA4DDE9D98D056529C253Ccampusfuberlinde_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable ... And it seems that Unicode is turned on (by default in VS11?!). To turn = it off see: http://stackoverflow.com/questions/1319461/how-do-i-turn-off-unicode-in-a-v= c-project David Von meinem iPad gesendet Am 10.05.2013 um 13:21 schrieb "Matthias Loose" >: Hello, I wanted to use SeqAn without the provided build system for just a couple f= unctions in a Project. Im using Visual Studio 11 right now and according to= this site: http://trac.seqan.de/wiki/BuildManual/IntegrationWithYourOwnBuildSystem all I need to do is include the seqan/include directory which I have done t= o a new Project. To test it Im using this file: #include #include // CharString, ... #include // to stream a CharString into cout int main(int, char const **) { std::cout << "Hello World!" << std::endl; seqan::CharString mySeqanString =3D "Hello SeqAn!"; std::cout << mySeqanString << std::endl; return 1; } Unfortunatly I get a lot of errors on build time. I attached the output to = this message. If I build the "first_app" using the provided build system it= builds fine, but for now Id rather juts use Seqan in my already started pr= oject and the prospect of just adding seqan to my includes seemes really ni= ce. Any help would be appreciated. Matthias Loose _______________________________________________ seqan-dev mailing list seqan-dev@lists.fu-berlin.de https://lists.fu-berlin.de/listinfo/seqan-dev --_000_C62692B903AA4DDE9D98D056529C253Ccampusfuberlinde_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable
... And it seems that Unico= de is turned on (by default in VS11?!). To turn it off see:

David

Von meinem iPad gesendet

Am 10.05.2013 um 13:21 schrieb "Matthias Loose" <studium@mindcode.de>:

Hello,

I wanted to use SeqAn without the provided build system for just a co= uple functions in a Project. Im using Visual Studio 11 right now and accord= ing to this site:

http://trac.seqan.de/wiki/BuildManual/IntegrationWithYourOwn= BuildSystem

all I need to do is include the seqan/include directory which I have = done to a new Project. To test it Im using this file:


#include <iostream>
#include <seqan/sequence.h>  // CharString, ...
#include <seqan/file.h>      // to str= eam a CharString into cout

int main(int, char const **)
{
std::cout << "Hello World!" << std::endl;
seqan::CharString mySeqanString =3D "Hello SeqAn!";<= br> std::cout << mySeqanString << std::endl;
return 1;
}

Unfortunatly I get a lot of errors on build time. I attached the outp= ut to this message. If I build the "first_app" using the provided= build system it builds fine, but for now Id rather juts use Seqan in my al= ready started project and the prospect of just adding seqan to my includes seemes really nice.

Any help would be appreciated.


Matthias Loose
<seqan_error.txt>
_______________________________________________
seqan-dev mailing list
seqan-dev@lists.fu-be= rlin.de
https://lis= ts.fu-berlin.de/listinfo/seqan-dev
--_000_C62692B903AA4DDE9D98D056529C253Ccampusfuberlinde_-- From s.henderson@ucl.ac.uk Tue May 14 13:16:27 2013 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UcDDW-0042mD-2L>; Tue, 14 May 2013 13:16:26 +0200 Received: from am1ehsobe004.messaging.microsoft.com ([213.199.154.207] helo=am1outboundpool.messaging.microsoft.com) by relay1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UcDDV-000hnF-Sl>; Tue, 14 May 2013 13:16:26 +0200 Received: from mail84-am1-R.bigfish.com (10.3.201.254) by AM1EHSOBE018.bigfish.com (10.3.207.140) with Microsoft SMTP Server id 14.1.225.23; Tue, 14 May 2013 11:16:23 +0000 Received: from mail84-am1 (localhost [127.0.0.1]) by mail84-am1-R.bigfish.com (Postfix) with ESMTP id 003E326055B for ; Tue, 14 May 2013 11:16:22 +0000 (UTC) X-Forefront-Antispam-Report: CIP:157.56.250.117; KIP:(null); UIP:(null); IPV:NLI; H:AMXPRD0111HT003.eurprd01.prod.exchangelabs.com; RD:none; EFVD:NLI X-SpamScore: 0 X-BigFish: PS0(zzc85dhzz1f42h1ee6h1de0h1d18h1fdah1202h1e76h1d1ah1d2ah1fc6hzz18c673hz2dh2a8h668h839hd25hf0ah1288h12a5h12bdh137ah1441h1504h1537h153bh15d0h162dh1631h1758h18e1h1946h19b5h19ceh1ad9h1b0ah1bceh1d07h1d0ch1d2eh1d3fh1155h) Received: from mail84-am1 (localhost.localdomain [127.0.0.1]) by mail84-am1 (MessageSwitch) id 1368530181630252_26620; Tue, 14 May 2013 11:16:21 +0000 (UTC) Received: from AM1EHSMHS003.bigfish.com (unknown [10.3.201.233]) by mail84-am1.bigfish.com (Postfix) with ESMTP id 925AB420065 for ; Tue, 14 May 2013 11:16:21 +0000 (UTC) Received: from AMXPRD0111HT003.eurprd01.prod.exchangelabs.com (157.56.250.117) by AM1EHSMHS003.bigfish.com (10.3.207.103) with Microsoft SMTP Server (TLS) id 14.1.225.23; Tue, 14 May 2013 11:16:20 +0000 Received: from AMXPRD0111MB472.eurprd01.prod.exchangelabs.com ([169.254.10.48]) by AMXPRD0111HT003.eurprd01.prod.exchangelabs.com ([10.242.12.164]) with mapi id 14.16.0311.000; Tue, 14 May 2013 11:16:20 +0000 From: "Henderson, Stephen" To: "seqan-dev@lists.fu-berlin.de" Thread-Topic: Finder and Pattern Thread-Index: Ac5QkY1rMkxFqo3cQmmujGGsVwHjPw== Date: Tue, 14 May 2013 11:16:20 +0000 Message-ID: <98456EB61783264C9A843890618267F84FEEC349@AMXPRD0111MB472.eurprd01.prod.exchangelabs.com> Accept-Language: en-GB, en-US Content-Language: en-GB X-MS-Has-Attach: X-MS-TNEF-Correlator: x-ucllive-sclrule: HASRUN Content-Type: multipart/alternative; boundary="_000_98456EB61783264C9A843890618267F84FEEC349AMXPRD0111MB472_" MIME-Version: 1.0 X-OriginatorOrg: ucl.ac.uk X-Originating-IP: 213.199.154.207 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1368530186-00000A3F-2B9EF889/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.419161, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=-0.7 required=5.0 tests=HTML_MESSAGE, RCVD_IN_DNSWL_LOW X-Spam-Checker-Version: SpamAssassin 3.3.3-zedat9255cc3 on Gabun.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] Finder and Pattern X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 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, 14 May 2013 11:16:27 -0000 --_000_98456EB61783264C9A843890618267F84FEEC349AMXPRD0111MB472_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi I have yet another question. I have used the countKmers function to read th= rough a fastq file and identify over-represented 5mers (e.g. AAAAA and TTTT= T commonly) e.g. std::vector< std::string > kmers I now want to plot their fraction at positions across the reads so I iterat= e through the fast records again trying to count any occurence of each of k= mer and it's position. This is essentially the last step of the fastQC prog= ram (though seqan seems a lot faster) i.e.: // more above NumericMatrix kmerMatrix(kmers.size(), numcycles-4); seqan::Dna5String seq; for( ; seqIt1 !=3D end(seqs); ++seqIt1) { seq =3D value(seqIt1); Finder finder(seq); for(unsigned i=3D0; i< kmers.size(); ++i) { Pattern pattern(kmers[i]); while (find(finder, pattern)) kmerMatrix(i,beginPosition(finder)) +=3D 1; } } return kmerMatrix; // this to be plot in R using ggplot2 } The above compiles fine and I think looks liek what I want but I get an odd= result with a 5mer skip. I see counts for the first kmer (AAAAA) at first = position, then 6th, 11th, 16th etc, The next kmer at 6th,11th, 16th and so on for all the other kmers: # this is the c++ function called from within R > kmerPlotCpp('test3.fastq', as.vector(kmers$kmers)) [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] = [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [1,] 1826 0 0 0 0 1189 0 0 0 0 1403 0 0 = 0 0 1371 0 0 0 0 1328 [2,] 0 0 0 0 0 641 0 0 0 0 482 0 0 = 0 0 504 0 0 0 0 493 [3,] 0 0 0 0 0 424 0 0 0 0 545 0 0 = 0 0 545 0 0 0 0 578 ... etc etc I don't understand why beginPosition(finder) is skipping in 5s. Do you? Also... is this the best approach? Is there a simpler/more efficient way? thx (Again) Stephen Henderson UCL Cancer Institute ps I have tried to clear(finder) at the end of the outer loop but this comp= iled and crashed runtime-- strangely? --_000_98456EB61783264C9A843890618267F84FEEC349AMXPRD0111MB472_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi
I have yet another question. I have used the countKmers function to re= ad through a fastq file and identify over-represented 5mers (e.g. AAAAA and= TTTTT commonly) e.g.  std::vector< std::string > kmers

I now want to plot their fraction at positions across the reads so I i= terate through the fast records again trying to count any occurence of each= of kmer and it's position. This is essentially the last step of the fastQC= program (though seqan seems a lot faster) i.e.:


// more above

NumericMatrix kmerMatrix(kmers.size(), numcycles-4);
seqan::Dna5String seq;         

    for( ; seqIt1 !=3D end(seqs); ++seqIt1)
    {
      seq =3D value(seqIt1);
      Finder<Dna5String> finder(seq);
      
      for(unsigned i=3D0;  i< kmers.size(); = 3;+i)
      {
       Pattern<Dna5String, Horspool> pattern= (kmers[i]);
        while (find(finder, pattern))
            kmerMatrix(i,beginPosition(f= inder)) +=3D 1;  
      }
    
    }  
  
    return kmerMatrix; // this to be plot in R using ggplot2=
}



The above compiles fine and I think looks liek what I want but I get a= n odd result with a 5mer skip. I see counts for the first kmer (AAAAA) at f= irst position, then 6th, 11th, 16th etc,


The next kmer at 6th,11th, 16th and so on for all the other kmers:&nbs= p;

# this is the c++ function called from within R
> kmerPlotCpp('test3.fastq', as.vector(kmers$kmers))

      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10= ] [,11] [,12] [,13] [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21]
 [1,] 1826    0    0    0   &n= bsp;0 1189    0    0    0     0 &nb= sp;1403     0     0     0     0 &nb= sp;1371     0     0     0     0 &nb= sp;1328
 [2,]    0    0    0    0=    0  641    0    0    0 &nbs= p;   0   482     0     0     0 &nbs= p;   0   504     0     0     0 &nbs= p;   0   493
 [3,]    0    0    0    0=    0  424    0    0    0 &nbs= p;   0   545     0     0     0 &nbs= p;   0   545     0     0     0 &nbs= p;   0   578
... etc etc


I don't understand why beginPosition(finder) is skipping in 5s. Do you= ?

Also... is this the best approach? Is there a simpler/more efficient w= ay?

thx (Again)
Stephen Henderson
UCL Cancer Institute

ps I have tried to clear(finder) at the end of the outer loop but this= compiled and crashed runtime-- strangely?
--_000_98456EB61783264C9A843890618267F84FEEC349AMXPRD0111MB472_-- From weese@campus.fu-berlin.de Thu May 16 09:57:36 2013 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Uct4B-001AAA-AR>; Thu, 16 May 2013 09:57:35 +0200 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Uct4B-003Zto-8V>; Thu, 16 May 2013 09:57:35 +0200 Received: from cas2.campus.fu-berlin.de ([130.133.170.202]) by relay2.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Uct4A-0008UI-RR>; Thu, 16 May 2013 09:57:35 +0200 Received: from EX02A.campus.fu-berlin.de ([130.133.170.132]) by CAS2.campus.fu-berlin.de ([130.133.170.202]) with mapi id 14.03.0123.003; Thu, 16 May 2013 09:57:33 +0200 From: "Weese, David" To: SeqAn Development Thread-Topic: [Seqan-dev] Finder and Pattern Thread-Index: Ac5QkY1rMkxFqo3cQmmujGGsVwHjPwBaLWyA Message-ID: <3C493D68-64BF-429A-B5ED-A0AB1B39E3B5@fu-berlin.de> References: <98456EB61783264C9A843890618267F84FEEC349@AMXPRD0111MB472.eurprd01.prod.exchangelabs.com> In-Reply-To: <98456EB61783264C9A843890618267F84FEEC349@AMXPRD0111MB472.eurprd01.prod.exchangelabs.com> Accept-Language: de-DE, en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: multipart/alternative; boundary="_000_3C493D6864BF429AB5EDA0AB1B39E3B5fuberlinde_" MIME-Version: 1.0 Date: Thu, 16 May 2013 09:57:32 +0200 X-Original-Date: Thu, 16 May 2013 07:57:32 +0000 X-Originating-IP: 130.133.170.202 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1368691055-00000A3F-16634833/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.075068, version=1.2.3 X-Spam-Flag: NO X-Spam-Status: No, score=-50.0 required=5.0 tests=ALL_TRUSTED,HTML_MESSAGE X-Spam-Checker-Version: SpamAssassin 3.3.3-zedat9255cc3 on Benin.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] Finder and Pattern X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 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, 16 May 2013 07:57:36 -0000 --_000_3C493D6864BF429AB5EDA0AB1B39E3B5fuberlinde_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi Stephen, mmh, I don't see why it shouldn't work. Maybe you can send us an example da= taset and your full source code for debugging. David -- David Weese weese@inf.fu-berlin.de Freie Universit=E4t Berlin http://www.inf.fu-berlin.de/ Institut f=FCr Informatik Phone: +49 30 838 75137 Takustra=DFe 9 Algorithmic Bioinformatics 14195 Berlin Room 020 Am 14.05.2013 um 13:16 schrieb "Henderson, Stephen" >: Hi I have yet another question. I have used the countKmers function to read th= rough a fastq file and identify over-represented 5mers (e.g. AAAAA and TTTT= T commonly) e.g. std::vector< std::string > kmers I now want to plot their fraction at positions across the reads so I iterat= e through the fast records again trying to count any occurence of each of k= mer and it's position. This is essentially the last step of the fastQC prog= ram (though seqan seems a lot faster) i.e.: // more above NumericMatrix kmerMatrix(kmers.size(), numcycles-4); seqan::Dna5String seq; for( ; seqIt1 !=3D end(seqs); ++seqIt1) { seq =3D value(seqIt1); Finder finder(seq); for(unsigned i=3D0; i< kmers.size(); ++i) { Pattern pattern(kmers[i]); while (find(finder, pattern)) kmerMatrix(i,beginPosition(finder)) +=3D 1; } } return kmerMatrix; // this to be plot in R using ggplot2 } The above compiles fine and I think looks liek what I want but I get an odd= result with a 5mer skip. I see counts for the first kmer (AAAAA) at first = position, then 6th, 11th, 16th etc, The next kmer at 6th,11th, 16th and so on for all the other kmers: # this is the c++ function called from within R > kmerPlotCpp('test3.fastq', as.vector(kmers$kmers)) [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] = [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [1,] 1826 0 0 0 0 1189 0 0 0 0 1403 0 0 = 0 0 1371 0 0 0 0 1328 [2,] 0 0 0 0 0 641 0 0 0 0 482 0 0 = 0 0 504 0 0 0 0 493 [3,] 0 0 0 0 0 424 0 0 0 0 545 0 0 = 0 0 545 0 0 0 0 578 ... etc etc I don't understand why beginPosition(finder) is skipping in 5s. Do you? Also... is this the best approach? Is there a simpler/more efficient way? thx (Again) Stephen Henderson UCL Cancer Institute ps I have tried to clear(finder) at the end of the outer loop but this comp= iled and crashed runtime-- strangely? _______________________________________________ seqan-dev mailing list seqan-dev@lists.fu-berlin.de https://lists.fu-berlin.de/listinfo/seqan-dev --_000_3C493D6864BF429AB5EDA0AB1B39E3B5fuberlinde_ Content-Type: text/html; charset="iso-8859-1" Content-ID: <11243176F471D747976A4D662A1DC2AE@campus.fu-berlin.de> Content-Transfer-Encoding: quoted-printable Hi Stephen,

mmh, I don't see why it shouldn't work. Maybe you can send us an examp= le dataset and your full source code for debugging.

David

--
David Weese weese@inf.fu-berlin.de Freie Universit=E4t Berlin http://www.inf.fu-berlin.de/
Institut f=FCr Informatik Phone: +49 30 838 75137
Takustra=DFe 9 = Algorithmic Bioinformatics
14195 Berlin Room 020

Am 14.05.2013 um 13:16 schrieb "Henderson, Stephen" <s.henderson@ucl.ac.uk>:

Hi
I have yet another question. I have used the countKmers function to re= ad through a fastq file and identify over-represented 5mers (e.g. AAAAA and= TTTTT commonly) e.g.  std::vector< std::string > kmers

I now want to plot their fraction at positions across the reads so I i= terate through the fast records again trying to count any occurence of each= of kmer and it's position. This is essentially the last step of the fastQC= program (though seqan seems a lot faster) i.e.:


// more above

NumericMatrix kmerMatrix(kmers.size(), numcycles-4);
seqan::Dna5String seq;         

    for( ; seqIt1 !=3D end(seqs); ++seqIt1)
    {
      seq =3D value(seqIt1);
      Finder<Dna5String> finder(seq);
      
      for(unsigned i=3D0;  i< kmers.size(); = 3;+i)
      {
       Pattern<Dna5String, Horspool> pattern= (kmers[i]);
        while (find(finder, pattern))
            kmerMatrix(i,beginPosition(f= inder)) +=3D 1;  
      }
    
    }  
  
    return kmerMatrix; // this to be plot in R using ggplot2=
}



The above compiles fine and I think looks liek what I want but I get a= n odd result with a 5mer skip. I see counts for the first kmer (AAAAA) at f= irst position, then 6th, 11th, 16th etc,


The next kmer at 6th,11th, 16th and so on for all the other kmers:&nbs= p;

# this is the c++ function called from within R
> kmerPlotCpp('test3.fastq', as.vector(kmers$kmers))

      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10= ] [,11] [,12] [,13] [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21]
 [1,] 1826    0    0    0   &n= bsp;0 1189    0    0    0     0 &nb= sp;1403     0     0     0     0 &nb= sp;1371     0     0     0     0 &nb= sp;1328
 [2,]    0    0    0    0=    0  641    0    0    0 &nbs= p;   0   482     0     0     0 &nbs= p;   0   504     0     0     0 &nbs= p;   0   493
 [3,]    0    0    0    0=    0  424    0    0    0 &nbs= p;   0   545     0     0     0 &nbs= p;   0   545     0     0     0 &nbs= p;   0   578
... etc etc


I don't understand why beginPosition(finder) is skipping in 5s. Do you= ?

Also... is this the best approach? Is there a simpler/more efficient w= ay?

thx (Again)
Stephen Henderson
UCL Cancer Institute

ps I have tried to clear(finder) at the end of the outer loop but this= compiled and crashed runtime-- strangely?
_______________________________________________
seqan-dev mailing list
seqan-dev@lists.fu-berlin.d= e
https://lists.fu-= berlin.de/listinfo/seqan-dev

--_000_3C493D6864BF429AB5EDA0AB1B39E3B5fuberlinde_-- From s.henderson@ucl.ac.uk Thu May 16 23:34:28 2013 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Ud5og-003Li5-SJ>; Thu, 16 May 2013 23:34:26 +0200 Received: from ch1ehsobe001.messaging.microsoft.com ([216.32.181.181] helo=ch1outboundpool.messaging.microsoft.com) by relay1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Ud5og-002blM-IF>; Thu, 16 May 2013 23:34:26 +0200 Received: from mail115-ch1-R.bigfish.com (10.43.68.231) by CH1EHSOBE006.bigfish.com (10.43.70.56) with Microsoft SMTP Server id 14.1.225.23; Thu, 16 May 2013 21:34:22 +0000 Received: from mail115-ch1 (localhost [127.0.0.1]) by mail115-ch1-R.bigfish.com (Postfix) with ESMTP id 69D3D360BE7 for ; Thu, 16 May 2013 21:34:22 +0000 (UTC) X-Forefront-Antispam-Report: CIP:157.56.250.117; KIP:(null); UIP:(null); IPV:NLI; H:AMXPRD0111HT001.eurprd01.prod.exchangelabs.com; RD:none; EFVD:NLI X-SpamScore: -8 X-BigFish: PS-8(zz148cIc85dh1432I179dNzz1f42h1ee6h1de0h1d18h1fdah1202h1e76h1d1ah1d2ah1fc6hzz17326ahz2dh2a8h668h839h944hd25hf0ah1220h1288h12a5h12a9h12bdh137ah13b6h1441h1504h1537h153bh15d0h162dh1631h1758h18e1h1946h19b5h19ceh1ad9h1b0ah1d07h1d0ch1d2eh1d3fh1155h) Received: from mail115-ch1 (localhost.localdomain [127.0.0.1]) by mail115-ch1 (MessageSwitch) id 1368740059126199_1794; Thu, 16 May 2013 21:34:19 +0000 (UTC) Received: from CH1EHSMHS032.bigfish.com (snatpool1.int.messaging.microsoft.com [10.43.68.246]) by mail115-ch1.bigfish.com (Postfix) with ESMTP id E9997300AAC for ; Thu, 16 May 2013 21:34:18 +0000 (UTC) Received: from AMXPRD0111HT001.eurprd01.prod.exchangelabs.com (157.56.250.117) by CH1EHSMHS032.bigfish.com (10.43.70.32) with Microsoft SMTP Server (TLS) id 14.1.225.23; Thu, 16 May 2013 21:34:17 +0000 Received: from AMXPRD0111MB472.eurprd01.prod.exchangelabs.com ([169.254.10.48]) by AMXPRD0111HT001.eurprd01.prod.exchangelabs.com ([10.242.12.162]) with mapi id 14.16.0311.000; Thu, 16 May 2013 21:34:13 +0000 From: "Henderson, Stephen" To: "seqan-dev@lists.fu-berlin.de" Thread-Topic: Finder and Pattern Thread-Index: AQHOUnkehTP1nB3Zi0a/D/H/m9Yjcw== Date: Thu, 16 May 2013 21:34:12 +0000 Message-ID: <98456EB61783264C9A843890618267F84FEED11C@AMXPRD0111MB472.eurprd01.prod.exchangelabs.com> Accept-Language: en-GB, en-US Content-Language: en-GB X-MS-Has-Attach: X-MS-TNEF-Correlator: x-ucllive-sclrule: HASRUN Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-OriginatorOrg: ucl.ac.uk X-Originating-IP: 216.32.181.181 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1368740066-00000A3F-0C539CD8/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.007812, version=1.2.3 X-Spam-Flag: NO X-Spam-Status: No, score=-0.7 required=5.0 tests=RCVD_IN_DNSWL_LOW X-Spam-Checker-Version: SpamAssassin 3.3.3-zedat9255cc3 on Botsuana.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] Finder and Pattern X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 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, 16 May 2013 21:34:28 -0000 Hi David=0A= =0A= Thanks for offering to look at the rest (again). I'm just trying to get the= hang of C++. A few points...=0A= =0A= 1) This maybe look odd as I am calling from and returning to R using RCpp l= ibraries. So NumericMatrix is an R/C++ type. I "think" this bit is working = as intended?? =0A= =0A= 2) My best guess is the problem is coercing a std::string kmers[i] to a Dna= 5String Pattern??=0A= =0A= i.e.=0A= Pattern pattern(kmers[i]);=0A= =0A= ...or maybe not??? It seems to have "worked"=0A= =0A= 3) The data I am using is ~the first 400K head of SRR031709.fastq I know it= doesn't have this odd pattern (i.e. it's not some artificial constructed t= est file) as I checked it with FastQC... and all the other stuff I tested w= ith this file works OK.=0A= =0A= =0A= #include =0A= #include =0A= #include =0A= #include =0A= #include =0A= #include =0A= =0A= using namespace Rcpp;=0A= using namespace seqan;=0A= =0A= // [[Rcpp::export]]=0A= =0A= NumericMatrix kmerPlot3Cpp(std::string argv, std::vector< std::string > kme= rs)=0A= { =0A= std::fstream in(argv.c_str(), std::ios::binary | std::ios::in);=0A= seqan::RecordReader > reader(in); = =0A= =0A= // Read file record-wise.=0A= seqan::CharString id;=0A= seqan::Dna5String seq;=0A= seqan::CharString qual;=0A= unsigned numreads =3D 0;=0A= =0A= // read single record to get the cycle length=0A= if (readRecord(id, seq, qual, reader, seqan::Fastq()) !=3D 0)=0A= return 1; // Could not record from file.=0A= unsigned numcycles=3D length(seq);=0A= =0A= NumericMatrix kmerMatrix(kmers.size(), numcycles-4); // presume 5 mers = =0A= =0A= =0A= while (!atEnd(reader))=0A= {=0A= if (readRecord(id, seq, qual, reader, seqan::Fastq()) !=3D 0)=0A= return 1; // Could not record from file.=0A= =0A= Finder finder(seq); =0A= for(unsigned i=3D0; i< kmers.size(); ++i)=0A= {=0A= Pattern pattern(kmers[i]);=0A= while (find(finder, pattern))=0A= {=0A= kmerMatrix(i,beginPosition(finder)) +=3D 1;=0A= }=0A= }=0A= =0A= } =0A= =0A= return kmerMatrix;=0A= }=0A= =0A= =0A= =0A= ...hmmm=0A= =0A= Stephen=0A= =0A= Message: 1=0A= Date: Thu, 16 May 2013 09:57:32 +0200=0A= From: "Weese, David" =0A= To: SeqAn Development =0A= Subject: Re: [Seqan-dev] Finder and Pattern=0A= Message-ID: <3C493D68-64BF-429A-B5ED-A0AB1B39E3B5@fu-berlin.de>=0A= Content-Type: text/plain; charset=3D"iso-8859-1"=0A= =0A= Hi Stephen,=0A= =0A= mmh, I don't see why it shouldn't work. Maybe you can send us an example da= taset and your full source code for debugging.=0A= =0A= David=0A= =0A= --=0A= David Weese weese@inf.fu-berlin.de=0A= Freie Universit?t Berlin http://www.inf.fu-berlin.de/=0A= Institut f?r Informatik Phone: +49 30 838 75137=0A= Takustra?e 9 Algorithmic Bioinformatics=0A= 14195 Berlin Room 020=0A= From jer15@hermes.cam.ac.uk Fri May 31 20:39:02 2013 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UiUE8-002Ap7-Ad>; Fri, 31 May 2013 20:39:00 +0200 Received: from ppsw-33.csi.cam.ac.uk ([131.111.8.133]) by relay1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UiUE8-001jU9-7i>; Fri, 31 May 2013 20:39:00 +0200 X-Cam-AntiVirus: no malware found X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ Received: from cpc6-dals15-2-0-cust115.hari.cable.virginmedia.com ([82.35.196.116]:55613 helo=[192.168.1.7]) by ppsw-33.csi.cam.ac.uk (smtp.hermes.cam.ac.uk [131.111.8.157]:587) with esmtpsa (PLAIN:jer15) (TLSv1:DHE-RSA-CAMELLIA256-SHA:256) id 1UiUE6-00034w-iD (Exim 4.80_167-5a66dd3) for seqan-dev@lists.fu-berlin.de (return-path ); Fri, 31 May 2013 19:38:58 +0100 Message-ID: <51A8EE42.8030805@mail.cryst.bbk.ac.uk> Date: Fri, 31 May 2013 19:38:58 +0100 From: John Reid User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:17.0) Gecko/20130510 Thunderbird/17.0.6 MIME-Version: 1.0 To: "seqan-dev@lists.fu-berlin.de" Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Sender: "J.E. Reid" X-Originating-IP: 131.111.8.133 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1370025540-00000A3F-47B75E40/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.355514, version=1.2.3 X-Spam-Flag: NO X-Spam-Status: No, score=-2.3 required=5.0 tests=RCVD_IN_DNSWL_MED X-Spam-Checker-Version: SpamAssassin 3.3.3-zedat9255cc3 on Burundi.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] Suffix links X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 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, 31 May 2013 18:39:02 -0000 Hi, I had a little google for this but I didn't find the answer. I have an algorithm which should run quickly on a suffix tree or array. However in the algorithm I will need to move from a node for say the suffix GCCGAA to the node for CCGAA. This is obviously expensive in a normal suffix tree. However I think that some suffix tree construction algorithms create suffix links (perhaps Ukkonen's algorithm) that do exactly this. Does SeqAn contain such algorithms and how can I access the suffix links after construction? Thanks, John.