From odenas@emory.edu Tue May 08 17:39:12 2012 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 <1SRmVL-0007oO-Sz>; Tue, 08 May 2012 17:39:12 +0200 Received: from ws-mr1.cc.emory.edu ([170.140.50.231]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1SRmVL-00038d-HJ>; Tue, 08 May 2012 17:39:11 +0200 Received: from e14edge1n.Emory.Edu (emoryfloatdmz.cc.emory.edu [170.140.52.254]) by ws-mr1.cc.emory.edu (8.13.8/8.13.1) with ESMTP id q48Fd6UY032712 for ; Tue, 8 May 2012 11:39:07 -0400 Received: from E14CH4W.Enterprise.emory.net (10.240.10.116) by e14edge1n.Emory.Edu (170.140.52.18) with Microsoft SMTP Server (TLS) id 14.2.283.3; Tue, 8 May 2012 11:39:06 -0400 Received: from E14MBX22N.Enterprise.emory.net ([fe80::8dd7:5f1:f61e:d718]) by e14ch4w.Enterprise.emory.net ([::1]) with mapi id 14.02.0283.003; Tue, 8 May 2012 11:39:06 -0400 From: "Denas, Olgert" To: "seqan-dev@lists.fu-berlin.de" Thread-Index: Ac0tMLNeCojETumdSp6twznJ57Sc4Q== Date: Tue, 8 May 2012 15:39:05 +0000 Message-ID: Accept-Language: en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Emory-MailScanner-Information: Please contact the ISP for more information X-Emory-MailScanner-ID: q48Fd6UY032712 X-Emory-MailScanner: Found to be clean X-Emory-MailScanner-SpamCheck: not spam, SpamAssassin (not cached, score=-0.01, required 8, autolearn=disabled, T_RP_MATCHES_RCVD -0.01) X-Emory-MailScanner-From: odenas@emory.edu X-Originating-IP: 170.140.50.231 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1336491551-00000D73-957A7FFA/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.015777, 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=2.0 required=5.0 tests=MISSING_SUBJECT, SPF_HELO_PASS, SPF_PASS,TO_ADDRESS_EQ_REAL Subject: [Seqan-dev] (no subject) 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, 08 May 2012 15:39:12 -0000 Hi, I am using the PISAtoolbox executables to analyze some biological data. I w= ant to use the models in ways other than generating new strings or scoring = strings. Is there any way to get access to the PISAtoolbox code? The next b= est thing would be a specification of the .vomc file so that I could parse = that myself. thanks, Olgert Denas ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). From bernd.jagla@pasteur.fr Fri May 11 13:33:40 2012 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 <1SSo6N-0000oO-VD>; Fri, 11 May 2012 13:33:40 +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 <1SSo6N-0007lP-RT>; Fri, 11 May 2012 13:33:39 +0200 Received: from maroilles.sis.pasteur.fr (localhost [127.0.0.1]) by mail-interne3.pasteur.fr (Postfix) with ESMTP id 2086038104F for ; Fri, 11 May 2012 13:33:38 +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 DA8B8381044 for ; Fri, 11 May 2012 13:33:37 +0200 (CEST) Message-ID: <4FACF90E.2040009@pasteur.fr> Date: Fri, 11 May 2012 13:33:34 +0200 From: Bernd Jagla User-Agent: Mozilla/5.0 (Windows NT 5.1; rv:12.0) Gecko/20120428 Thunderbird/12.0.1 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::1336736019-00000D73-94DB9B6F/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 Benin.ZEDAT.FU-Berlin.DE X-Spam-Level: x X-Spam-Status: No, score=1.4 required=5.0 tests=DNS_FROM_RFC_POST Subject: [Seqan-dev] raserS2 question 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, 11 May 2012 11:33:40 -0000 Hi, I am using rasers2 with the following command line options: core/apps/razers2/razers2 -id -o ${fp%.bowtie.*}.razers2.sam -of 4 -ed ${fp%.bowtie.*}.razers2.ed $fastaFile $fqFile It seems to consume more than 50GB of memory. Is there a way to restrict/control the memory consumption? Is the memory consumption predictable? What parameters does it depend on? Thanks clarifying these points, Best, Bernd From bernd.jagla@pasteur.fr Wed May 16 09:55:29 2012 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 <1SUZ4y-0005DS-Ho>; Wed, 16 May 2012 09:55:28 +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 <1SUZ4y-0004wr-Dg>; Wed, 16 May 2012 09:55:28 +0200 Received: from maroilles.sis.pasteur.fr (localhost [127.0.0.1]) by mail-interne3.pasteur.fr (Postfix) with ESMTP id B21E538104C for ; Wed, 16 May 2012 09:55:26 +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 881B4381044 for ; Wed, 16 May 2012 09:55:26 +0200 (CEST) Message-ID: <4FB35D71.3050506@pasteur.fr> Date: Wed, 16 May 2012 09:55:29 +0200 From: Bernd Jagla User-Agent: Mozilla/5.0 (Windows NT 5.1; rv:12.0) Gecko/20120428 Thunderbird/12.0.1 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::1337154928-00000D73-52132669/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.373256, 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 X-Spam-Status: No, score=1.4 required=5.0 tests=DNS_FROM_RFC_POST Subject: [Seqan-dev] mapQ overwritten when writing sam/bam? 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: Wed, 16 May 2012 07:55:29 -0000 Hi, I am using the sam/bam packages to read and write sam/bam files and I noticed that a value for the mapping quality (column 5) has been changed from 255 to 0... Is this possible? I am using the BamIOContext as in the following example: template int writeOutRecordSet(TStream &fp, StringSet recSet, BamIOContext > & context, TFormat const & tag, ROI & roi) { unsigned maxC = 0; for (unsigned i = 0; i < length(roi.count); i++) { if (maxC < roi.count[i]) maxC = roi.count[i]; } roi.countMax = maxC; for (unsigned i = 0; i < length(recSet); i++) { BamTagsDict tagDict(recSet[i].tags); setTagValue(tagDict, "rl", roi.len); setTagValue(tagDict, "ri", roi.min); setTagValue(tagDict, "rx", roi.max); setTagValue(tagDict, "ry", maxC); setTagValue(tagDict, "rn", length(recSet), 'i'); write2(fp, recSet[i], context, tag); } return maxC; } What do I have to do to keep the value? Thanks a lot for your kind support. Best, Bernd From hauswedell@mi.fu-berlin.de Wed May 16 10:37:29 2012 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 <1SUZjc-0006fi-BH>; Wed, 16 May 2012 10:37:28 +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 <1SUZjc-0007md-5S>; Wed, 16 May 2012 10:37:28 +0200 Received: from [202.127.20.13] (helo=[10.10.118.79]) by inpost2.zedat.fu-berlin.de (Exim 4.69) with esmtpsa (envelope-from ) id <1SUZjb-0001Uw-RF>; Wed, 16 May 2012 10:37:28 +0200 Message-ID: <4FB36743.3010503@mi.fu-berlin.de> Date: Wed, 16 May 2012 16:37:23 +0800 From: Hannes Hauswedell User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:12.0) Gecko/20120430 Thunderbird/12.0.1 MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de References: <4F97BEFF.3000302@pasteur.fr>, In-Reply-To: Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit X-Originating-IP: 202.127.20.13 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1337157448-00000D73-ACFDCC26/0-0/0-0 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 Botsuana.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-1.8 required=5.0 tests=ALL_TRUSTED, RCVD_IN_NJABL_PROXY Subject: Re: [Seqan-dev] reading fasta with non-DNA5 characters 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: Wed, 16 May 2012 08:37:29 -0000 Hi, it all depends on what type of String you give to the recordReader. It is designed to check for the SequenceType's alphabet and use that as a criterium, so the following should fail on non-ACGTN: CharString seqIds; Dna5String faSeqs; RecordReader >, DoublePass > refReader(seqMMapString); int read2out = read2(seqIds, faSeqs, refReader, Fasta()); but the following should accept any alphabetical[1]: CharString seqIds; CharString faSeqs; RecordReader >, DoublePass > refReader(seqMMapString); int read2out = read2(seqIds, faSeqs, refReader, Fasta()); This won't however convert anything. That could be done later, maybe using ModifiedString<> to avoid copying. Regards, Hannes [1] I just checked that because I want to read a sequence including gaps, which fails (because '-' is non alphabetical --working on patch--). However the mentioned characters Y and M should not be a problem. On 04/26/2012 06:29 AM, Holtgrewe, Manuel wrote: > If I remember correctly, the interface will not allow you to read non-ACGTN characters when using read(..., Fasta()) but return an error value != 0 in this case. > > Bernd, what you can do right now is to load your reads into CharStrings and convert them to Dna5. > > In the long term, I guess we will need more control for the users over I/O behaviour. At the moment, the assumptions are fairly conservative, e.g. do not allow non-ACTG(N) characters for Dna(5) and tailored to what you find in NGS reads and whole genome data. > > Cheers, > Manuel > ________________________________________ > From: Weese, David [weese@campus.fu-berlin.de] > Sent: Wednesday, April 25, 2012 10:44 PM > To: SeqAn Development > Subject: Re: [Seqan-dev] reading fasta with non-DNA5 characters > > Hi, > > actually it should automatically convert every non-ACGT character to N (or A for Dna targets). Have you already tried reading your files into string over Dna5 alphabets? > > Cheers, > David > -- > David Weese weese@inf.fu-berlin.de > Freie Universität Berlin http://www.inf.fu-berlin.de/ > Institut für Informatik Phone: +49 30 838 75246 > Takustraße 9 Algorithmic Bioinformatics > 14195 Berlin Room 021 > > Am 25.04.2012 um 11:08 schrieb Bernd Jagla: > >> Hi, >> >> I have a couple of genome seqeunces that contain characters other than ACTGN (i.e. Y, M,...)... >> >> Is there a way to read those sequences in as well and automatically convert those non conforming letters to N? >> >> Thanks, >> >> Bernd >> >> PS: >> >> I am using: >> >> RecordReader >, DoublePass > refReader(seqMMapString); >> int read2out = read2(seqIds, faSeqs, refReader, Fasta()); >> >> for reading in the data and get an INVALID_FORMAT error... >> >> >> _______________________________________________ >> 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 > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev From manuel.holtgrewe@fu-berlin.de Wed May 16 11:18:58 2012 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 <1SUaNl-00087o-Ew>; Wed, 16 May 2012 11:18:57 +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 <1SUaNl-0004ft-66>; Wed, 16 May 2012 11:18:57 +0200 Received: from cas3.campus.fu-berlin.de ([130.133.170.203]) by relay2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1SUaNk-0007q6-Vc>; Wed, 16 May 2012 11:18:57 +0200 Received: from EX02A.campus.fu-berlin.de ([130.133.170.132]) by CAS3.campus.fu-berlin.de ([130.133.170.203]) with mapi id 14.02.0298.004; Wed, 16 May 2012 11:18:55 +0200 From: "Holtgrewe, Manuel" To: SeqAn Development Thread-Topic: [Seqan-dev] mapQ overwritten when writing sam/bam? Thread-Index: AQHNMzlInjjMteNj6UarkIE4oA6AypbMIkbH Date: Wed, 16 May 2012 09:18:54 +0000 Message-ID: References: <4FB35D71.3050506@pasteur.fr> In-Reply-To: <4FB35D71.3050506@pasteur.fr> Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Originating-IP: 130.133.170.203 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1337159937-00000D73-6D5233D0/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.049032, 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] mapQ overwritten when writing sam/bam? 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: Wed, 16 May 2012 09:18:58 -0000 Hi Bernd,=0A= =0A= what do you mean it is changed? Is the wrong value written to the file? Is = it changed in the program itself? Are you writing SAM or BAM?=0A= =0A= Can you provide a minimal program that shows the problem?=0A= =0A= Second, I guess the function signature should be:=0A= =0A= template=0A= int writeOutRecordSet(TStream &fp, String const & recSe= t,=0A= BamIOContext > & context, TFormat const & = =0A= tag,=0A= ROI & roi) {=0A= =0A= - StringSet & recSet -> String cons= t & recSet=0A= =0A= Cheers!=0A= Manuel=0A= ________________________________________=0A= From: Bernd Jagla [bernd.jagla@pasteur.fr]=0A= Sent: Wednesday, May 16, 2012 9:55 AM=0A= To: seqan-dev@lists.fu-berlin.de=0A= Subject: [Seqan-dev] mapQ overwritten when writing sam/bam?=0A= =0A= Hi,=0A= =0A= I am using the sam/bam packages to read and write sam/bam files and I=0A= noticed that a value for the mapping quality (column 5) has been changed=0A= from 255 to 0...=0A= Is this possible? I am using the BamIOContext as in the following example:= =0A= =0A= template=0A= int writeOutRecordSet(TStream &fp, StringSet recSet,=0A= BamIOContext > & context, TFormat const &=0A= tag,=0A= ROI & roi) {=0A= =0A= unsigned maxC =3D 0;=0A= for (unsigned i =3D 0; i < length(roi.count); i++) {=0A= if (maxC < roi.count[i])=0A= maxC =3D roi.count[i];=0A= }=0A= roi.countMax =3D maxC;=0A= for (unsigned i =3D 0; i < length(recSet); i++) {=0A= BamTagsDict tagDict(recSet[i].tags);=0A= setTagValue(tagDict, "rl", roi.len);=0A= setTagValue(tagDict, "ri", roi.min);=0A= setTagValue(tagDict, "rx", roi.max);=0A= setTagValue(tagDict, "ry", maxC);=0A= setTagValue(tagDict, "rn", length(recSet), 'i');=0A= write2(fp, recSet[i], context, tag);=0A= }=0A= return maxC;=0A= }=0A= =0A= What do I have to do to keep the value?=0A= =0A= Thanks a lot for your kind support.=0A= =0A= Best,=0A= =0A= Bernd=0A= =0A= =0A= _______________________________________________=0A= seqan-dev mailing list=0A= seqan-dev@lists.fu-berlin.de=0A= https://lists.fu-berlin.de/listinfo/seqan-dev=0A= From bernd.jagla@pasteur.fr Wed May 16 14:43:37 2012 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 <1SUdZo-0007XI-R3>; Wed, 16 May 2012 14:43:36 +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 <1SUdZo-0005TN-NI>; Wed, 16 May 2012 14:43:36 +0200 Received: from maroilles.sis.pasteur.fr (localhost [127.0.0.1]) by mail-interne3.pasteur.fr (Postfix) with ESMTP id 5B23F381053 for ; Wed, 16 May 2012 14:43:34 +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 34E64381052 for ; Wed, 16 May 2012 14:43:32 +0200 (CEST) Message-ID: <4FB3A0F7.2080709@pasteur.fr> Date: Wed, 16 May 2012 14:43:35 +0200 From: Bernd Jagla User-Agent: Mozilla/5.0 (Windows NT 5.1; rv:12.0) Gecko/20120428 Thunderbird/12.0.1 MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de References: <4FB35D71.3050506@pasteur.fr> In-Reply-To: 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::1337172216-00000D73-B49A35CB/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.070972, 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 X-Spam-Status: No, score=1.4 required=5.0 tests=DNS_FROM_RFC_POST Subject: Re: [Seqan-dev] mapQ overwritten when writing sam/bam? 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: Wed, 16 May 2012 12:43:38 -0000 Hi, sorry, it seems the problem is on my side... Thanks for looking into it, though, Cheers, Bernd On 5/16/2012 11:18 AM, Holtgrewe, Manuel wrote: > Hi Bernd, > > what do you mean it is changed? Is the wrong value written to the file? Is it changed in the program itself? Are you writing SAM or BAM? > > Can you provide a minimal program that shows the problem? > > Second, I guess the function signature should be: > > template > int writeOutRecordSet(TStream&fp, String const& recSet, > BamIOContext > & context, TFormat const& > tag, > ROI& roi) { > > - StringSet & recSet -> String const& recSet > > Cheers! > Manuel > ________________________________________ > From: Bernd Jagla [bernd.jagla@pasteur.fr] > Sent: Wednesday, May 16, 2012 9:55 AM > To: seqan-dev@lists.fu-berlin.de > Subject: [Seqan-dev] mapQ overwritten when writing sam/bam? > > Hi, > > I am using the sam/bam packages to read and write sam/bam files and I > noticed that a value for the mapping quality (column 5) has been changed > from 255 to 0... > Is this possible? I am using the BamIOContext as in the following example: > > template > int writeOutRecordSet(TStream&fp, StringSet recSet, > BamIOContext > & context, TFormat const& > tag, > ROI& roi) { > > unsigned maxC = 0; > for (unsigned i = 0; i< length(roi.count); i++) { > if (maxC< roi.count[i]) > maxC = roi.count[i]; > } > roi.countMax = maxC; > for (unsigned i = 0; i< length(recSet); i++) { > BamTagsDict tagDict(recSet[i].tags); > setTagValue(tagDict, "rl", roi.len); > setTagValue(tagDict, "ri", roi.min); > setTagValue(tagDict, "rx", roi.max); > setTagValue(tagDict, "ry", maxC); > setTagValue(tagDict, "rn", length(recSet), 'i'); > write2(fp, recSet[i], context, tag); > } > return maxC; > } > > What do I have to do to keep the value? > > Thanks a lot for your kind support. > > Best, > > 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 hauswedell@mi.fu-berlin.de Mon May 21 09:38:23 2012 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 <1SWNC9-0001rL-S3>; Mon, 21 May 2012 09:38:22 +0200 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 <1SWNC9-0001ez-NS>; Mon, 21 May 2012 09:38:21 +0200 Received: from [202.127.20.13] (helo=[10.10.118.79]) by inpost2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtpsa (envelope-from ) id <1SWNC9-0005MW-DI>; Mon, 21 May 2012 09:38:21 +0200 Message-ID: <4FB9F0EA.3090304@mi.fu-berlin.de> Date: Mon, 21 May 2012 15:38:18 +0800 From: Hannes Hauswedell User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:12.0) Gecko/20120430 Thunderbird/12.0.1 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: 202.127.20.13 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1337585901-00000D73-692EB357/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000786, 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=-1.8 required=5.0 tests=ALL_TRUSTED, RCVD_IN_NJABL_PROXY Subject: [Seqan-dev] Blosum80 Matrix 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: Mon, 21 May 2012 07:38:23 -0000 Hey everyone, the Blosum80 used internally in seqan is this one: http://www.cbcb.umd.edu/confcour/CMSC423-materials/BLOSUM80.txt which says "Matrix made by matblas from blosum80_3.iij" However most other references to Blosum80 on the web refer to this one: http://www.cs.ucf.edu/courses/cap5937/fall2004/assignment2/BLOSUM80 which says "Matrix made by matblas from blosum80.iij" They do differ quite a bit. Does anyone know the background? Why was one chosen over the other? Regards, Hannes From Sabrina.Krakau@fu-berlin.de Wed May 23 16:00:47 2012 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.69) with esmtp (envelope-from ) id <1SXC7J-000076-Fr>; Wed, 23 May 2012 16:00:45 +0200 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.69) with esmtp (envelope-from ) id <1SXC7J-0000hI-By>; Wed, 23 May 2012 16:00:45 +0200 Received: from cas1.campus.fu-berlin.de ([130.133.170.201]) by relay2.zedat.fu-berlin.de (Exim 4.69) with esmtp (envelope-from ) id <1SXC7J-0001r6-3w>; Wed, 23 May 2012 16:00:45 +0200 Received: from EX03A.campus.fu-berlin.de ([130.133.170.134]) by CAS1.campus.fu-berlin.de ([130.133.170.201]) with mapi id 14.02.0298.004; Wed, 23 May 2012 16:00:42 +0200 From: "Krakau, Sabrina" To: "Krakau, Sabrina" Thread-Topic: SeqAn - BioStore Workshop 2012, Berlin, September the 4th - 7th Thread-Index: AQHNOOxwt52dnK1WD062ZpUtibWXyg== Date: Wed, 23 May 2012 14:00:41 +0000 Message-ID: <8219DAA8-4879-4C89-8239-CAE9BA7DC4FF@fu-berlin.de> Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: yes X-MS-TNEF-Correlator: Content-Type: multipart/related; boundary="_005_8219DAA848794C898239CAE9BA7DC4FFfuberlinde_"; type="multipart/alternative" MIME-Version: 1.0 X-Originating-IP: 130.133.170.201 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1337781645-00000D73-EE151E12/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.007840, 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=-2.6 required=5.0 tests=ALL_TRUSTED, EXTRA_MPART_TYPE, HTML_MESSAGE Cc: AG ABI ABI , SeqAn Development , "seqan-interests@lists.fu-berlin.de" Subject: [Seqan-dev] SeqAn - BioStore Workshop 2012, Berlin, September the 4th - 7th 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: Wed, 23 May 2012 14:00:47 -0000 --_005_8219DAA848794C898239CAE9BA7DC4FFfuberlinde_ Content-Type: multipart/alternative; boundary="_000_8219DAA848794C898239CAE9BA7DC4FFfuberlinde_" --_000_8219DAA848794C898239CAE9BA7DC4FFfuberlinde_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear SeqAn Users and Developers, We would like to invite you to the SeqAn - BioStore Workshop 2012 in Berlin= . It will take place in the time from Tuesday the 4th of September to Friday = the 7th of September (the Friday is to be confirmed). So please mark this dates in your calendar. The workshop will be addressed to both SeqAn beginners and advanced SeqAn d= evelopers. The rough content will be: - Overview of SeqAn, its highlights and new features - External talks - Tutorials for beginners and for advanced developers in a different range = of subjects. Additionally there will be time for the discussion of new ideas and hands-o= n sessions. Please forward this invitation to your colleagues or any interested users. More detailed information will follow soon. By then you can also visit our BioStore project website: http://www.seqan-biostore.de/wp/seqan-workshops/2012-seqan-workshop/ and our SeqAn website: www.seqan.de We hope to see you in September, The SeqAn Team [cid:12D5553D-AD16-40D5-986F-BF6FABF0587B] [cid:53AF5887-D1F2-4BAA-BF6C-C= F01BF1C6DB7] Sabrina Krakau Freie Universit=E4t Berlin Institute of Computer Science Algorithmic Bioinformatics - Project BioStore Takustr. 9, 14195 Berlin Telefon: +49 (0)30 838 75228 --_000_8219DAA848794C898239CAE9BA7DC4FFfuberlinde_ Content-Type: text/html; charset="iso-8859-1" Content-ID: Content-Transfer-Encoding: quoted-printable

Dear SeqAn Users and Developers,

We would like to invite you to the SeqAn - BioStore Workshop 2012 in Berlin= . 
It will take place in the time from Tuesday the 4th of September to Friday = the 7th of September (the Friday is to be confirmed).
So please mark this dates in your calendar.

The workshop will be addressed to both SeqAn beginners and advanced SeqAn d= evelopers. 

The rough content will be:
- Overview of SeqAn, its highlights and new features
- External talks
- Tutorials for beginners and for advanced developers in a different range = of subjects.

Additionally there will be time for the discussion of new ideas and hands-o= n sessions.

Please forward this invitation to your colleagues or any interested users.<= br>
More detailed information will follow soon.
By then you can also visit our BioStore project website:
and our SeqAn website:
www.seqan.de


We hope to see you in September,

The SeqAn Team

 


<= span class=3D"Apple-style-span" style=3D"border-collapse: separate; color: = rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: nor= mal; font-weight: normal; letter-spacing: normal; line-height: normal; orph= ans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; w= hite-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal= -spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decoratio= ns-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-wid= th: 0px; font-size: medium; ">   

Sabrina Krakau

Freie Universit=E4t Berlin
Institute of Computer Science
Algorithmic Bioinformatics - Project BioStore

Takustr. 9, 14195 Berlin
Telefon: +49 (0)30 838 75228 =


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0n3ldov5Wzrw2FBpITkFU9TmumWuG87vnfG+8WnnXXZ4vqSVh0QkdtSR0nMWms1Gc5nY/9/Gu9zD eF9hZpdHRCGyYgrj74e2spKHJ/xe0ci3CjgL2Z7tAagKnN2kcJ4FWXP/G7Tg3ejfbcz7mga71qEz DwwUn6dgcRcNO7K5kL4+PI93bQe3fHHZTwtHSgEk0SAFiCpmV+qvC+N5ru24PA28VgM4XCKK0OhI IUUe6+FdB8b7XwrdK73wetB5f43he743tvt2dN73z4e+I8bzfL+c5zsXtqw6aWH/mYTDfj173/8I MADOw7X/kZPH9QAAAABJRU5ErkJggg== --_005_8219DAA848794C898239CAE9BA7DC4FFfuberlinde_-- From njjustice@gmail.com Mon May 28 02:32:39 2012 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 <1SYnsz-0003s3-NS>; Mon, 28 May 2012 02:32:37 +0200 Received: from mail-lb0-f182.google.com ([209.85.217.182]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1SYnsz-0002eR-H6>; Mon, 28 May 2012 02:32:37 +0200 Received: by lbon10 with SMTP id n10so2173913lbo.13 for ; Sun, 27 May 2012 17:32:36 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:date:message-id:subject:from:to:content-type; bh=pflfOrCRBPulQp4jGnS2EPllnyacpodlTZWt0fiq3Bo=; b=gw42ODVxt8UQQy4IvprFXuljqwvSSoKOTWgOarivHOgshu/nshWxANmFnGaS4u9Sip RtCvTvk71uVROTwJIraXe0dHeBz9jf8AuAtODBRnEbNXYKdVpnkJESrX3xsiNRtpfCCn 1OSfH5mJthZnckHwOkU0dc1xrOwHI8tEi6k9n3Vi5mZb4k+vrqdKFiCuzPowPkST9LqQ QOfQeeC4R9SOS8j345amnsoB4xZpDQHncS3ASmjZVB+9scBw2680JZd3ZJXebddZk1fK 7gzQWz3o78F9rIw5fwQOJ/11WJRaxvxYU3zCq2g636a30PE0laxl+/dUhbMaFAw5f3L2 JT6g== MIME-Version: 1.0 Received: by 10.152.135.200 with SMTP id pu8mr6443125lab.8.1338165155995; Sun, 27 May 2012 17:32:35 -0700 (PDT) Received: by 10.112.65.38 with HTTP; Sun, 27 May 2012 17:32:35 -0700 (PDT) Date: Sun, 27 May 2012 19:32:35 -0500 Message-ID: From: Neil Justice To: seqan-dev@lists.fu-berlin.de Content-Type: multipart/mixed; boundary=f46d04374547c620e804c10ddaaa X-Originating-IP: 209.85.217.182 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1338165157-00000D73-77867534/0-0/0-0 X-Bogosity: Unsure, tests=bogofilter, spamicity=0.499601, 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 X-Spam-Status: No, score=1.9 required=5.0 tests=DNS_FROM_RFC_ABUSE, FU_BOGO_UNSURE,RCVD_BY_IP,SPF_HELO_PASS,SPF_PASS Subject: [Seqan-dev] I'm interested in making SeqAn faster but am stopped by these CMake errors 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: Mon, 28 May 2012 00:32:39 -0000 --f46d04374547c620e804c10ddaaa Content-Type: text/plain; charset=ISO-8859-1 Hello SeqAn developers, My name is Neil Justice and I'm interested in helping advance genetics research by contributing my programming skills to the task of making SeqAn faster. I work on performance tuning the C++ of a high-frequency algorithmic trading program at a hedge fund in Houston. Lately I've been interested in finding an interesting and good-for-humanity open source project to work on at home, and SeqAn appears to be that project. I am on Windows and am trying to generate a Visual Studio 2008 .sln for SeqAn using CMake. I've pulled the code using svn per tutorial http://trac.seqan.de/wiki/Tutorial/GettingStarted. Here are the CMake errors I encounter in response to CMake command "cmake C:\Seqan\seqan-trunk -G "Visual Studio 9 2008"" (errors also attached as a screenshot): PS C:\Seqan\build> cmake C:\Seqan\seqan-trunk -G "Visual Studio 9 2008" -- Check for working C compiler using: Visual Studio 9 2008 -- Check for working C compiler using: Visual Studio 9 2008 -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler using: Visual Studio 9 2008 -- Check for working CXX compiler using: Visual Studio 9 2008 -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done SEQAN_CONTRIB_BASE is undefined! -- CMAKE_FIND_ROOT_PATH is "". -- Found PythonInterp: C:/Python32/python.exe (found version "3.2.3") -- Zlib could not be found! -- BZip2 libraries could not be found! -- Try OpenMP C flag = [/openmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Success -- Try OpenMP CXX flag = [/openmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Success -- Performing Test TR1_SHARED_PTR_USE_TR1_MEMORY -- Performing Test TR1_SHARED_PTR_USE_TR1_MEMORY - Failed -- Performing Test TR1_SHARED_PTR_USE_MEMORY -- Performing Test TR1_SHARED_PTR_USE_MEMORY - Success -- Performing Test TR1_UNORDERED_MAP_USE_TR1_UNORDERED_MAP -- Performing Test TR1_UNORDERED_MAP_USE_TR1_UNORDERED_MAP - Failed -- Performing Test TR1_UNORDERED_MAP_USE_UNORDERED_MAP -- Performing Test TR1_UNORDERED_MAP_USE_UNORDERED_MAP - Success -- Could NOT find Boost -- Looking for include file execinfo.h -- Looking for include file execinfo.h - not found. -- INFO: Rabema not build because zlib was not found. CMake Error at core/apps/rabema/CMakeLists.txt:43 (install): install TARGETS given target "rabema_build_gold_standard" which does not exist in this directory. -- Boost not found, not building snp_store. -- Configuring incomplete, errors occurred! PS C:\Seqan\build> PS C:\Seqan\build> How would you fix these errors? I don't have Zlib or BZip2 (do I need to download these libraries?). I have Boost (which was not found - do I need to specify its path somewhere?). I have Python (which was found). Thanks and I look forward to finding some SeqAn performance issues. 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AhYtNHd10EiKEQEiQARuFYERFkSwiIu1vt3nzVgpGwXfoBA6zTuQ3tcqgpnPvCRga+TOpx4BTYg4 ESK5RxkiQASIAI4Af0f014I7riYHm4SXzqzgHdFUD4kQT25KEgEiQARSBNDfjmmKwDtyoFh8C1RP SMIMPWaBM5nJfCnnaQZql6TsNZEFh7FNs4ECRIAIEIF7QwBlwbTKC+BEpTb/bFQUXOuti5AKci3i V+DL8SxICry3LUp/iQARWIrAKhY8GY2MZZ5vKbvsYTjk2ioxp2yK0HYMmnh3aVpQOREgAkTgThDg 74hGzwXFLdmeh9rNWH2T1iQz7+ZtcD4lxTvJUbpJBIgAEViHwC3/dgxvHq7LG2omAkSACNwGAjfL gnrGuo2A0QsiQASIABGYiMD/D/dhgmqwvaDjAAAAAElFTkSuQmCC --f46d04374547c620e804c10ddaaa-- From manuel.holtgrewe@fu-berlin.de Mon May 28 12:14:47 2012 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 <1SYwyL-0003g1-Q5>; Mon, 28 May 2012 12:14:45 +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 <1SYwyL-0000NB-Mx>; Mon, 28 May 2012 12:14:45 +0200 Received: from cas1.campus.fu-berlin.de ([130.133.170.201]) by relay2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1SYwyL-0005qx-DC>; Mon, 28 May 2012 12:14:45 +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 14.02.0298.004; Mon, 28 May 2012 12:14:44 +0200 From: "Holtgrewe, Manuel" To: SeqAn Development Thread-Topic: [Seqan-dev] I'm interested in making SeqAn faster but am stopped by these CMake errors Thread-Index: AQHNPGlrFx65/zgRp0uFjerdZHue1Zbe6Tfo Date: Mon, 28 May 2012 10:14:43 +0000 Message-ID: References: In-Reply-To: Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Originating-IP: 130.133.170.201 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1338200085-00000D73-09CF78F6/0-0/0-0 X-Bogosity: Unsure, tests=bogofilter, spamicity=0.492923, 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=-1.3 required=5.0 tests=ALL_TRUSTED,FU_BOGO_UNSURE Subject: Re: [Seqan-dev] I'm interested in making SeqAn faster but am stopped by these CMake errors 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: Mon, 28 May 2012 10:14:47 -0000 Dear Neil,=0A= =0A= the problem is caused by a bug in one of the CMakeLists.txt files. This sho= uld be corrected now.=0A= =0A= As for zlib/bzlib, you can simply install prebuilt versions of these librar= ies:=0A= =0A= https://trac.seqan.de/wiki/HowTo/InstallContribsWindows=0A= =0A= Most of the library will also work without zlib, but for reading BAM files = or compressed streams, you will need it. This is also explained in some det= ail in some messages after the configuration.=0A= =0A= Cheers,=0A= Manuel=0A= ________________________________________=0A= From: Neil Justice [njjustice@gmail.com]=0A= Sent: Monday, May 28, 2012 2:32 AM=0A= To: seqan-dev@lists.fu-berlin.de=0A= Subject: [Seqan-dev] I'm interested in making SeqAn faster but am stopped b= y these CMake errors=0A= =0A= Hello SeqAn developers,=0A= =0A= My name is Neil Justice and I'm interested in helping advance genetics=0A= research by contributing my programming skills to the task of making=0A= SeqAn faster. I work on performance tuning the C++ of a high-frequency=0A= algorithmic trading program at a hedge fund in Houston. Lately I've=0A= been interested in finding an interesting and good-for-humanity open=0A= source project to work on at home, and SeqAn appears to be that=0A= project.=0A= =0A= I am on Windows and am trying to generate a Visual Studio 2008 .sln=0A= for SeqAn using CMake. I've pulled the code using svn per tutorial=0A= http://trac.seqan.de/wiki/Tutorial/GettingStarted. Here are the CMake=0A= errors I encounter in response to CMake command "cmake=0A= C:\Seqan\seqan-trunk -G "Visual Studio 9 2008"" (errors also attached=0A= as a screenshot):=0A= =0A= PS C:\Seqan\build> cmake C:\Seqan\seqan-trunk -G "Visual Studio 9 2008"=0A= -- Check for working C compiler using: Visual Studio 9 2008=0A= -- Check for working C compiler using: Visual Studio 9 2008 -- works=0A= -- Detecting C compiler ABI info=0A= -- Detecting C compiler ABI info - done=0A= -- Check for working CXX compiler using: Visual Studio 9 2008=0A= -- Check for working CXX compiler using: Visual Studio 9 2008 -- works=0A= -- Detecting CXX compiler ABI info=0A= -- Detecting CXX compiler ABI info - done=0A= SEQAN_CONTRIB_BASE is undefined!=0A= -- CMAKE_FIND_ROOT_PATH is "".=0A= -- Found PythonInterp: C:/Python32/python.exe (found version "3.2.3")=0A= -- Zlib could not be found!=0A= -- BZip2 libraries could not be found!=0A= -- Try OpenMP C flag =3D [/openmp]=0A= -- Performing Test OpenMP_FLAG_DETECTED=0A= -- Performing Test OpenMP_FLAG_DETECTED - Success=0A= -- Try OpenMP CXX flag =3D [/openmp]=0A= -- Performing Test OpenMP_FLAG_DETECTED=0A= -- Performing Test OpenMP_FLAG_DETECTED - Success=0A= -- Performing Test TR1_SHARED_PTR_USE_TR1_MEMORY=0A= -- Performing Test TR1_SHARED_PTR_USE_TR1_MEMORY - Failed=0A= -- Performing Test TR1_SHARED_PTR_USE_MEMORY=0A= -- Performing Test TR1_SHARED_PTR_USE_MEMORY - Success=0A= -- Performing Test TR1_UNORDERED_MAP_USE_TR1_UNORDERED_MAP=0A= -- Performing Test TR1_UNORDERED_MAP_USE_TR1_UNORDERED_MAP - Failed=0A= -- Performing Test TR1_UNORDERED_MAP_USE_UNORDERED_MAP=0A= -- Performing Test TR1_UNORDERED_MAP_USE_UNORDERED_MAP - Success=0A= -- Could NOT find Boost=0A= -- Looking for include file execinfo.h=0A= -- Looking for include file execinfo.h - not found.=0A= -- INFO: Rabema not build because zlib was not found.=0A= CMake Error at core/apps/rabema/CMakeLists.txt:43 (install):=0A= install TARGETS given target "rabema_build_gold_standard" which does not= =0A= exist in this directory.=0A= =0A= -- Boost not found, not building snp_store.=0A= -- Configuring incomplete, errors occurred!=0A= PS C:\Seqan\build>=0A= PS C:\Seqan\build>=0A= =0A= How would you fix these errors? I don't have Zlib or BZip2 (do I need=0A= to download these libraries?). I have Boost (which was not found - do=0A= I need to specify its path somewhere?). I have Python (which was=0A= found).=0A= =0A= Thanks and I look forward to finding some SeqAn performance issues.=0A= =0A= Neil= From njjustice@gmail.com Thu May 31 06:12:08 2012 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 <1SZwk1-0007zw-NF>; Thu, 31 May 2012 06:12:05 +0200 Received: from mail-lpp01m010-f54.google.com ([209.85.215.54]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1SZwk1-0005lJ-Iw>; Thu, 31 May 2012 06:12:05 +0200 Received: by laai10 with SMTP id i10so505004laa.13 for ; Wed, 30 May 2012 21:12:04 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:in-reply-to:references:date:message-id:subject:from:to :content-type:content-transfer-encoding; bh=x0gR3n9B9pVI8700TYtFG7mjYI0fii6TKrAr4tDdXDc=; b=lStkwUDSPsITujjmdiwl0XwSqwUQz6d9QeYDMfXW2NFMHdfruMqtbKwrWYmFNBHImE o3S8FLTsYhD23oxnr9tPbryfbval54/kS2Mm9ofZ2LZt7KheyfJbDlTQ1SOTD34ECvKZ swz3M8HlF32HpfRvY09cGKhSiy3f5T7DUC5yP/UdtMe5DMwVyf2TwlR6/UGQ1Fnz3Y44 tk0jhzCkm3A3dPHKqLSsQl+stYcwc9lfVvzYJjiLAkDiNm/kTxqhTQ/8w7INqz3+HIbZ butDqFw1etlhRtbmRMroDhQsRV1STg9pVA33jFtVOZsPVF2nbC9CK1ikaQsBMRJh/4qW WpeQ== MIME-Version: 1.0 Received: by 10.152.105.173 with SMTP id gn13mr18100357lab.20.1338437523991; Wed, 30 May 2012 21:12:03 -0700 (PDT) Received: by 10.112.65.38 with HTTP; Wed, 30 May 2012 21:12:03 -0700 (PDT) In-Reply-To: References: Date: Wed, 30 May 2012 23:12:03 -0500 Message-ID: From: Neil Justice To: seqan-dev@lists.fu-berlin.de Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable X-Originating-IP: 209.85.215.54 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1338437525-00000D73-BD8EF5A3/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.001299, 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=0.4 required=5.0 tests=DNS_FROM_RFC_ABUSE, RCVD_BY_IP, SPF_HELO_PASS,SPF_PASS Subject: Re: [Seqan-dev] seqan-dev Digest, Vol 32, Issue 8 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, 31 May 2012 04:12:08 -0000 Thanks Manuel. Your fix to that CMakeLists.txt file allowed me to run CMake without error and generate an .sln file. The code now builds for me except for these four compiler errors: error C3861: 'Bam': identifier not found c:\Seqan\seqan-trunk\extras\demos\bam_library_size.cpp 244 error C2665: 'open' : none of the 8 overloads could convert all the argument types c:\Seqan\seqan-trunk\extras\demos\bam_library_size.cpp 238 error C2079: 'inBamStream' uses undefined class 'seqan::Stream' c:\Seqan\seqan-trunk\extras\demos\bam_library_size.cpp 237 error C2065: 'Bgzf' : undeclared identifier c:\Seqan\seqan-trunk\extras\demos\bam_library_size.cpp 237 How are these errors resolved? Assuming these errors are resolved by obtaining zlib/bzlib: link https://trac.seqan.de/wiki/HowTo/InstallContribsWindows leads to a login/password prompt for FU Berlin for which I have no login or password. Is there another link to zlib/bzlib? Also, which files contain the most performance-sensitive code? Cheers, Neil On Tue, May 29, 2012 at 5:00 AM, wr= ote: > Send seqan-dev mailing list submissions to > =A0 =A0 =A0 =A0seqan-dev@lists.fu-berlin.de > > To subscribe or unsubscribe via the World Wide Web, visit > =A0 =A0 =A0 =A0https://lists.fu-berlin.de/listinfo/seqan-dev > or, via email, send a message with subject or body 'help' to > =A0 =A0 =A0 =A0seqan-dev-request@lists.fu-berlin.de > > You can reach the person managing the list at > =A0 =A0 =A0 =A0seqan-dev-owner@lists.fu-berlin.de > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of seqan-dev digest..." > > > Today's Topics: > > =A0 1. Re: I'm interested in making SeqAn faster but am stopped by > =A0 =A0 =A0these CMake errors (Holtgrewe, Manuel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 28 May 2012 10:14:43 +0000 > From: "Holtgrewe, Manuel" > To: SeqAn Development > Subject: Re: [Seqan-dev] I'm interested in making SeqAn faster but am > =A0 =A0 =A0 =A0stopped by =A0 =A0 =A0these CMake errors > Message-ID: > =A0 =A0 =A0 =A0 > Content-Type: text/plain; charset=3D"us-ascii" > > Dear Neil, > > the problem is caused by a bug in one of the CMakeLists.txt files. This s= hould be corrected now. > > As for zlib/bzlib, you can simply install prebuilt versions of these libr= aries: > > https://trac.seqan.de/wiki/HowTo/InstallContribsWindows > > Most of the library will also work without zlib, but for reading BAM file= s or compressed streams, you will need it. This is also explained in some d= etail in some messages after the configuration. > > Cheers, > Manuel > ________________________________________ > From: Neil Justice [njjustice@gmail.com] > Sent: Monday, May 28, 2012 2:32 AM > To: seqan-dev@lists.fu-berlin.de > Subject: [Seqan-dev] I'm interested in making SeqAn faster but am stopped= by =A0 =A0these CMake errors > > Hello SeqAn developers, > > My name is Neil Justice and I'm interested in helping advance genetics > research by contributing my programming skills to the task of making > SeqAn faster. I work on performance tuning the C++ of a high-frequency > algorithmic trading program at a hedge fund in Houston. Lately I've > been interested in finding an interesting and good-for-humanity open > source project to work on at home, and SeqAn appears to be that > project. > > I am on Windows and am trying to generate a Visual Studio 2008 .sln > for SeqAn using CMake. I've pulled the code using svn per tutorial > http://trac.seqan.de/wiki/Tutorial/GettingStarted. Here are the CMake > errors I encounter in response to CMake command "cmake > C:\Seqan\seqan-trunk -G "Visual Studio 9 2008"" (errors also attached > as a screenshot): > > PS C:\Seqan\build> cmake C:\Seqan\seqan-trunk -G "Visual Studio 9 2008" > -- Check for working C compiler using: Visual Studio 9 2008 > -- Check for working C compiler using: Visual Studio 9 2008 -- works > -- Detecting C compiler ABI info > -- Detecting C compiler ABI info - done > -- Check for working CXX compiler using: Visual Studio 9 2008 > -- Check for working CXX compiler using: Visual Studio 9 2008 -- works > -- Detecting CXX compiler ABI info > -- Detecting CXX compiler ABI info - done > SEQAN_CONTRIB_BASE is undefined! > -- CMAKE_FIND_ROOT_PATH is "". > -- Found PythonInterp: C:/Python32/python.exe (found version "3.2.3") > -- Zlib could not be found! > -- BZip2 libraries could not be found! > -- Try OpenMP C flag =3D [/openmp] > -- Performing Test OpenMP_FLAG_DETECTED > -- Performing Test OpenMP_FLAG_DETECTED - Success > -- Try OpenMP CXX flag =3D [/openmp] > -- Performing Test OpenMP_FLAG_DETECTED > -- Performing Test OpenMP_FLAG_DETECTED - Success > -- Performing Test TR1_SHARED_PTR_USE_TR1_MEMORY > -- Performing Test TR1_SHARED_PTR_USE_TR1_MEMORY - Failed > -- Performing Test TR1_SHARED_PTR_USE_MEMORY > -- Performing Test TR1_SHARED_PTR_USE_MEMORY - Success > -- Performing Test TR1_UNORDERED_MAP_USE_TR1_UNORDERED_MAP > -- Performing Test TR1_UNORDERED_MAP_USE_TR1_UNORDERED_MAP - Failed > -- Performing Test TR1_UNORDERED_MAP_USE_UNORDERED_MAP > -- Performing Test TR1_UNORDERED_MAP_USE_UNORDERED_MAP - Success > -- Could NOT find Boost > -- Looking for include file execinfo.h > -- Looking for include file execinfo.h - not found. > -- INFO: Rabema not build because zlib was not found. > CMake Error at core/apps/rabema/CMakeLists.txt:43 (install): > =A0install TARGETS given target "rabema_build_gold_standard" which does n= ot > =A0exist in this directory. > > -- Boost not found, not building snp_store. > -- Configuring incomplete, errors occurred! > PS C:\Seqan\build> > PS C:\Seqan\build> > > How would you fix these errors? I don't have Zlib or BZip2 (do I need > to download these libraries?). I have Boost (which was not found - do > I need to specify its path somewhere?). I have Python (which was > found). > > Thanks and I look forward to finding some SeqAn performance issues. > > Neil > > > ------------------------------ > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev > > > End of seqan-dev Digest, Vol 32, Issue 8 > **************************************** From rwan@cuhk.edu.hk Thu May 31 06:37:12 2012 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 <1SZx8H-0000Mz-2H>; Thu, 31 May 2012 06:37:09 +0200 Received: from cmt1.itsc.cuhk.edu.hk ([137.189.11.91]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1SZx8G-0000X6-LO>; Thu, 31 May 2012 06:37:09 +0200 Received: from [137.189.51.48] (unknown [137.189.51.48]) (using TLSv1 with cipher DHE-RSA-AES256-SHA (256/256 bits)) (No client certificate requested) (Authenticated sender: b126594) by cmt1.itsc.cuhk.edu.hk (Postfix) with ESMTPSA id 918DA298195; Thu, 31 May 2012 12:37:02 +0800 (HKT) Message-ID: <4FC6F570.7030902@cuhk.edu.hk> Date: Thu, 31 May 2012 12:37:04 +0800 From: Raymond Wan User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:12.0) Gecko/20120430 Thunderbird/12.0.1 MIME-Version: 1.0 To: SeqAn Development References: In-Reply-To: Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Originating-IP: 137.189.11.91 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1338439029-00000D73-3CF61C4C/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.196441, 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: Re: [Seqan-dev] seqan-dev Digest, Vol 32, Issue 8 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, 31 May 2012 04:37:12 -0000 Hi Neil, On Thursday, May 31, 2012 12:12 PM, Neil Justice wrote: > error C3861: 'Bam': identifier not > found c:\Seqan\seqan-trunk\extras\demos\bam_library_size.cpp 244 > error C2665: 'open' : none of the 8 overloads could convert all the > argument types c:\Seqan\seqan-trunk\extras\demos\bam_library_size.cpp 238 > error C2079: 'inBamStream' uses undefined class > 'seqan::Stream' c:\Seqan\seqan-trunk\extras\demos\bam_library_size.cpp 237 > error C2065: 'Bgzf' : undeclared > identifier c:\Seqan\seqan-trunk\extras\demos\bam_library_size.cpp 237 I think this is a problem with building the demos -- it doesn't necessarily mean that you have a problem with your Seqan installation... > Assuming these errors are resolved by obtaining zlib/bzlib: link > https://trac.seqan.de/wiki/HowTo/InstallContribsWindows leads to a > login/password prompt for FU Berlin for which I have no login or > password. Is there another link to zlib/bzlib? zlib and bzlib are public. Try digging around: http://zlib.net/ http://www.bzip.org/ for library versions that are suitable for Windows. After you install them, you should check that CMake can indeed find them. That's unrelated to Seqan -- for example, skim over this message about getting Zlib to work under Windows with CMake: http://www.cmake.org/pipermail/cmake/2006-October/011466.html > Also, which files contain the most performance-sensitive code? Quite frankly, if there was a section of code that was performance-sensitive and they knew about it, I think the Seqan developers (which, BTW, is not me) would have spotted it and fixed it. :-D On the other hand, they may have something on their to-do list that they never got around to fixing... Ray From manuel.holtgrewe@fu-berlin.de Thu May 31 08:47:57 2012 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 <1SZzAp-0004M2-Kf>; Thu, 31 May 2012 08:47:55 +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 <1SZzAp-0005lB-HK>; Thu, 31 May 2012 08:47:55 +0200 Received: from cas3.campus.fu-berlin.de ([130.133.170.203]) by relay2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1SZzAp-0007EH-9R>; Thu, 31 May 2012 08:47:55 +0200 Received: from EX02A.campus.fu-berlin.de ([130.133.170.132]) by CAS3.campus.fu-berlin.de ([130.133.170.203]) with mapi id 14.02.0298.004; Thu, 31 May 2012 08:47:54 +0200 From: "Holtgrewe, Manuel" To: SeqAn Development Thread-Topic: [Seqan-dev] seqan-dev Digest, Vol 32, Issue 8 Thread-Index: AQHNPuOSgnRNWAG9MkW/w0un4ZU4w5bjc/EP Date: Thu, 31 May 2012 06:47:54 +0000 Message-ID: References: , In-Reply-To: Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Originating-IP: 130.133.170.203 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1338446875-00000D73-389BD576/0-0/0-0 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 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] seqan-dev Digest, Vol 32, Issue 8 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, 31 May 2012 06:47:57 -0000 Hi Neal, sorry for providing the HTTPS link. The correct link is:=0A= =0A= http://trac.seqan.de/wiki/HowTo/InstallContribsWindows=0A= =0A= The SeqAn Trac is publically available via HTTP.=0A= =0A= I'll send another email about performance sensitive code later after a disc= ussion with colleagues.=0A= =0A= Cheers,=0A= Manuel=0A= ________________________________________=0A= From: Neil Justice [njjustice@gmail.com]=0A= Sent: Thursday, May 31, 2012 6:12 AM=0A= To: seqan-dev@lists.fu-berlin.de=0A= Subject: Re: [Seqan-dev] seqan-dev Digest, Vol 32, Issue 8=0A= =0A= Thanks Manuel. Your fix to that CMakeLists.txt file allowed me to run=0A= CMake without error and generate an .sln file.=0A= =0A= The code now builds for me except for these four compiler errors:=0A= =0A= error C3861: 'Bam': identifier not=0A= found c:\Seqan\seqan-trunk\extras\demos\bam_library_size.cpp 244=0A= error C2665: 'open' : none of the 8 overloads could convert all the=0A= argument types c:\Seqan\seqan-trunk\extras\demos\bam_library_size.cpp 238= =0A= error C2079: 'inBamStream' uses undefined class=0A= 'seqan::Stream' c:\Seqan\seqan-trunk\extras\demos\bam_library_size.cpp 237= =0A= error C2065: 'Bgzf' : undeclared=0A= identifier c:\Seqan\seqan-trunk\extras\demos\bam_library_size.cpp 237= =0A= =0A= How are these errors resolved?=0A= =0A= Assuming these errors are resolved by obtaining zlib/bzlib: link=0A= https://trac.seqan.de/wiki/HowTo/InstallContribsWindows leads to a=0A= login/password prompt for FU Berlin for which I have no login or=0A= password. Is there another link to zlib/bzlib?=0A= =0A= Also, which files contain the most performance-sensitive code?=0A= =0A= Cheers,=0A= Neil=0A= =0A= On Tue, May 29, 2012 at 5:00 AM, wr= ote:=0A= > Send seqan-dev mailing list submissions to=0A= > seqan-dev@lists.fu-berlin.de=0A= >=0A= > To subscribe or unsubscribe via the World Wide Web, visit=0A= > https://lists.fu-berlin.de/listinfo/seqan-dev=0A= > or, via email, send a message with subject or body 'help' to=0A= > seqan-dev-request@lists.fu-berlin.de=0A= >=0A= > You can reach the person managing the list at=0A= > seqan-dev-owner@lists.fu-berlin.de=0A= >=0A= > When replying, please edit your Subject line so it is more specific=0A= > than "Re: Contents of seqan-dev digest..."=0A= >=0A= >=0A= > Today's Topics:=0A= >=0A= > 1. Re: I'm interested in making SeqAn faster but am stopped by=0A= > these CMake errors (Holtgrewe, Manuel)=0A= >=0A= >=0A= > ----------------------------------------------------------------------=0A= >=0A= > Message: 1=0A= > Date: Mon, 28 May 2012 10:14:43 +0000=0A= > From: "Holtgrewe, Manuel" =0A= > To: SeqAn Development =0A= > Subject: Re: [Seqan-dev] I'm interested in making SeqAn faster but am=0A= > stopped by these CMake errors=0A= > Message-ID:=0A= > = =0A= > Content-Type: text/plain; charset=3D"us-ascii"=0A= >=0A= > Dear Neil,=0A= >=0A= > the problem is caused by a bug in one of the CMakeLists.txt files. This s= hould be corrected now.=0A= >=0A= > As for zlib/bzlib, you can simply install prebuilt versions of these libr= aries:=0A= >=0A= > https://trac.seqan.de/wiki/HowTo/InstallContribsWindows=0A= >=0A= > Most of the library will also work without zlib, but for reading BAM file= s or compressed streams, you will need it. This is also explained in some d= etail in some messages after the configuration.=0A= >=0A= > Cheers,=0A= > Manuel=0A= > ________________________________________=0A= > From: Neil Justice [njjustice@gmail.com]=0A= > Sent: Monday, May 28, 2012 2:32 AM=0A= > To: seqan-dev@lists.fu-berlin.de=0A= > Subject: [Seqan-dev] I'm interested in making SeqAn faster but am stopped= by these CMake errors=0A= >=0A= > Hello SeqAn developers,=0A= >=0A= > My name is Neil Justice and I'm interested in helping advance genetics=0A= > research by contributing my programming skills to the task of making=0A= > SeqAn faster. I work on performance tuning the C++ of a high-frequency=0A= > algorithmic trading program at a hedge fund in Houston. Lately I've=0A= > been interested in finding an interesting and good-for-humanity open=0A= > source project to work on at home, and SeqAn appears to be that=0A= > project.=0A= >=0A= > I am on Windows and am trying to generate a Visual Studio 2008 .sln=0A= > for SeqAn using CMake. I've pulled the code using svn per tutorial=0A= > http://trac.seqan.de/wiki/Tutorial/GettingStarted. Here are the CMake=0A= > errors I encounter in response to CMake command "cmake=0A= > C:\Seqan\seqan-trunk -G "Visual Studio 9 2008"" (errors also attached=0A= > as a screenshot):=0A= >=0A= > PS C:\Seqan\build> cmake C:\Seqan\seqan-trunk -G "Visual Studio 9 2008"= =0A= > -- Check for working C compiler using: Visual Studio 9 2008=0A= > -- Check for working C compiler using: Visual Studio 9 2008 -- works=0A= > -- Detecting C compiler ABI info=0A= > -- Detecting C compiler ABI info - done=0A= > -- Check for working CXX compiler using: Visual Studio 9 2008=0A= > -- Check for working CXX compiler using: Visual Studio 9 2008 -- works=0A= > -- Detecting CXX compiler ABI info=0A= > -- Detecting CXX compiler ABI info - done=0A= > SEQAN_CONTRIB_BASE is undefined!=0A= > -- CMAKE_FIND_ROOT_PATH is "".=0A= > -- Found PythonInterp: C:/Python32/python.exe (found version "3.2.3")=0A= > -- Zlib could not be found!=0A= > -- BZip2 libraries could not be found!=0A= > -- Try OpenMP C flag =3D [/openmp]=0A= > -- Performing Test OpenMP_FLAG_DETECTED=0A= > -- Performing Test OpenMP_FLAG_DETECTED - Success=0A= > -- Try OpenMP CXX flag =3D [/openmp]=0A= > -- Performing Test OpenMP_FLAG_DETECTED=0A= > -- Performing Test OpenMP_FLAG_DETECTED - Success=0A= > -- Performing Test TR1_SHARED_PTR_USE_TR1_MEMORY=0A= > -- Performing Test TR1_SHARED_PTR_USE_TR1_MEMORY - Failed=0A= > -- Performing Test TR1_SHARED_PTR_USE_MEMORY=0A= > -- Performing Test TR1_SHARED_PTR_USE_MEMORY - Success=0A= > -- Performing Test TR1_UNORDERED_MAP_USE_TR1_UNORDERED_MAP=0A= > -- Performing Test TR1_UNORDERED_MAP_USE_TR1_UNORDERED_MAP - Failed=0A= > -- Performing Test TR1_UNORDERED_MAP_USE_UNORDERED_MAP=0A= > -- Performing Test TR1_UNORDERED_MAP_USE_UNORDERED_MAP - Success=0A= > -- Could NOT find Boost=0A= > -- Looking for include file execinfo.h=0A= > -- Looking for include file execinfo.h - not found.=0A= > -- INFO: Rabema not build because zlib was not found.=0A= > CMake Error at core/apps/rabema/CMakeLists.txt:43 (install):=0A= > install TARGETS given target "rabema_build_gold_standard" which does not= =0A= > exist in this directory.=0A= >=0A= > -- Boost not found, not building snp_store.=0A= > -- Configuring incomplete, errors occurred!=0A= > PS C:\Seqan\build>=0A= > PS C:\Seqan\build>=0A= >=0A= > How would you fix these errors? I don't have Zlib or BZip2 (do I need=0A= > to download these libraries?). I have Boost (which was not found - do=0A= > I need to specify its path somewhere?). I have Python (which was=0A= > found).=0A= >=0A= > Thanks and I look forward to finding some SeqAn performance issues.=0A= >=0A= > Neil=0A= >=0A= >=0A= > ------------------------------=0A= >=0A= > _______________________________________________=0A= > seqan-dev mailing list=0A= > seqan-dev@lists.fu-berlin.de=0A= > https://lists.fu-berlin.de/listinfo/seqan-dev=0A= >=0A= >=0A= > End of seqan-dev Digest, Vol 32, Issue 8=0A= > ****************************************=0A= =0A= _______________________________________________=0A= seqan-dev mailing list=0A= seqan-dev@lists.fu-berlin.de=0A= https://lists.fu-berlin.de/listinfo/seqan-dev=0A= From Jochen.Singer@fu-berlin.de Thu May 31 09:49:00 2012 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 <1Sa07u-0006GF-6m>; Thu, 31 May 2012 09:48:58 +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 <1Sa07u-0000A0-3X>; Thu, 31 May 2012 09:48:58 +0200 Received: from cas1.campus.fu-berlin.de ([130.133.170.201]) by relay2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Sa07t-0003pm-TW>; Thu, 31 May 2012 09:48:58 +0200 Received: from EX01B.campus.fu-berlin.de ([130.133.170.131]) by CAS1.campus.fu-berlin.de ([130.133.170.201]) with mapi id 14.02.0298.004; Thu, 31 May 2012 09:48:57 +0200 From: "Singer, Jochen" To: SeqAn Development Thread-Topic: [Seqan-dev] seqan-dev Digest, Vol 32, Issue 8 Thread-Index: AQHNPuOSx3fMBAj2jUG5O7WOOD+aC5bjU00AgAARDgA= Date: Thu, 31 May 2012 07:48:56 +0000 Message-ID: <0A95298C-87A4-436C-8CC0-B4D7B76A9D6A@campus.fu-berlin.de> References: , In-Reply-To: Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: text/plain; charset="iso-8859-1" Content-ID: <06DC4A66981EBF46A0E16D6D557386BA@campus.fu-berlin.de> Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Originating-IP: 130.133.170.201 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1338450538-00000D73-B432E191/0-0/0-0 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 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] seqan-dev Digest, Vol 32, Issue 8 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, 31 May 2012 07:49:00 -0000 Hi Manuel, ich wollte dich nur fragen, ob ihr mir bescheid sagen k=F6nnte, wenn ihr eu= ch f=FCr code entscheidet, da ich so auch sehe, welche teile sensibel sind = :-) On 31.05.2012, at 08:47, Holtgrewe, Manuel wrote: > Hi Neal, sorry for providing the HTTPS link. The correct link is: >=20 > http://trac.seqan.de/wiki/HowTo/InstallContribsWindows >=20 > The SeqAn Trac is publically available via HTTP. >=20 > I'll send another email about performance sensitive code later after a di= scussion with colleagues. >=20 > Cheers, > Manuel > ________________________________________ > From: Neil Justice [njjustice@gmail.com] > Sent: Thursday, May 31, 2012 6:12 AM > To: seqan-dev@lists.fu-berlin.de > Subject: Re: [Seqan-dev] seqan-dev Digest, Vol 32, Issue 8 >=20 > Thanks Manuel. Your fix to that CMakeLists.txt file allowed me to run > CMake without error and generate an .sln file. >=20 > The code now builds for me except for these four compiler errors: >=20 > error C3861: 'Bam': identifier not > found c:\Seqan\seqan-trunk\extras\demos\bam_library_size.cpp 244 > error C2665: 'open' : none of the 8 overloads could convert all the > argument types c:\Seqan\seqan-trunk\extras\demos\bam_library_size.cpp 2= 38 > error C2079: 'inBamStream' uses undefined class > 'seqan::Stream' c:\Seqan\seqan-trunk\extras\demos\bam_library_size.cpp 2= 37 > error C2065: 'Bgzf' : undeclared > identifier c:\Seqan\seqan-trunk\extras\demos\bam_library_size.cpp 2= 37 >=20 > How are these errors resolved? >=20 > Assuming these errors are resolved by obtaining zlib/bzlib: link > https://trac.seqan.de/wiki/HowTo/InstallContribsWindows leads to a > login/password prompt for FU Berlin for which I have no login or > password. Is there another link to zlib/bzlib? >=20 > Also, which files contain the most performance-sensitive code? >=20 > Cheers, > Neil >=20 > On Tue, May 29, 2012 at 5:00 AM, = wrote: >> Send seqan-dev mailing list submissions to >> seqan-dev@lists.fu-berlin.de >>=20 >> To subscribe or unsubscribe via the World Wide Web, visit >> https://lists.fu-berlin.de/listinfo/seqan-dev >> or, via email, send a message with subject or body 'help' to >> seqan-dev-request@lists.fu-berlin.de >>=20 >> You can reach the person managing the list at >> seqan-dev-owner@lists.fu-berlin.de >>=20 >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of seqan-dev digest..." >>=20 >>=20 >> Today's Topics: >>=20 >> 1. Re: I'm interested in making SeqAn faster but am stopped by >> these CMake errors (Holtgrewe, Manuel) >>=20 >>=20 >> ---------------------------------------------------------------------- >>=20 >> Message: 1 >> Date: Mon, 28 May 2012 10:14:43 +0000 >> From: "Holtgrewe, Manuel" >> To: SeqAn Development >> Subject: Re: [Seqan-dev] I'm interested in making SeqAn faster but am >> stopped by these CMake errors >> Message-ID: >> >> Content-Type: text/plain; charset=3D"us-ascii" >>=20 >> Dear Neil, >>=20 >> the problem is caused by a bug in one of the CMakeLists.txt files. This = should be corrected now. >>=20 >> As for zlib/bzlib, you can simply install prebuilt versions of these lib= raries: >>=20 >> https://trac.seqan.de/wiki/HowTo/InstallContribsWindows >>=20 >> Most of the library will also work without zlib, but for reading BAM fil= es or compressed streams, you will need it. This is also explained in some = detail in some messages after the configuration. >>=20 >> Cheers, >> Manuel >> ________________________________________ >> From: Neil Justice [njjustice@gmail.com] >> Sent: Monday, May 28, 2012 2:32 AM >> To: seqan-dev@lists.fu-berlin.de >> Subject: [Seqan-dev] I'm interested in making SeqAn faster but am stoppe= d by these CMake errors >>=20 >> Hello SeqAn developers, >>=20 >> My name is Neil Justice and I'm interested in helping advance genetics >> research by contributing my programming skills to the task of making >> SeqAn faster. I work on performance tuning the C++ of a high-frequency >> algorithmic trading program at a hedge fund in Houston. Lately I've >> been interested in finding an interesting and good-for-humanity open >> source project to work on at home, and SeqAn appears to be that >> project. >>=20 >> I am on Windows and am trying to generate a Visual Studio 2008 .sln >> for SeqAn using CMake. I've pulled the code using svn per tutorial >> http://trac.seqan.de/wiki/Tutorial/GettingStarted. Here are the CMake >> errors I encounter in response to CMake command "cmake >> C:\Seqan\seqan-trunk -G "Visual Studio 9 2008"" (errors also attached >> as a screenshot): >>=20 >> PS C:\Seqan\build> cmake C:\Seqan\seqan-trunk -G "Visual Studio 9 2008" >> -- Check for working C compiler using: Visual Studio 9 2008 >> -- Check for working C compiler using: Visual Studio 9 2008 -- works >> -- Detecting C compiler ABI info >> -- Detecting C compiler ABI info - done >> -- Check for working CXX compiler using: Visual Studio 9 2008 >> -- Check for working CXX compiler using: Visual Studio 9 2008 -- works >> -- Detecting CXX compiler ABI info >> -- Detecting CXX compiler ABI info - done >> SEQAN_CONTRIB_BASE is undefined! >> -- CMAKE_FIND_ROOT_PATH is "". >> -- Found PythonInterp: C:/Python32/python.exe (found version "3.2.3") >> -- Zlib could not be found! >> -- BZip2 libraries could not be found! >> -- Try OpenMP C flag =3D [/openmp] >> -- Performing Test OpenMP_FLAG_DETECTED >> -- Performing Test OpenMP_FLAG_DETECTED - Success >> -- Try OpenMP CXX flag =3D [/openmp] >> -- Performing Test OpenMP_FLAG_DETECTED >> -- Performing Test OpenMP_FLAG_DETECTED - Success >> -- Performing Test TR1_SHARED_PTR_USE_TR1_MEMORY >> -- Performing Test TR1_SHARED_PTR_USE_TR1_MEMORY - Failed >> -- Performing Test TR1_SHARED_PTR_USE_MEMORY >> -- Performing Test TR1_SHARED_PTR_USE_MEMORY - Success >> -- Performing Test TR1_UNORDERED_MAP_USE_TR1_UNORDERED_MAP >> -- Performing Test TR1_UNORDERED_MAP_USE_TR1_UNORDERED_MAP - Failed >> -- Performing Test TR1_UNORDERED_MAP_USE_UNORDERED_MAP >> -- Performing Test TR1_UNORDERED_MAP_USE_UNORDERED_MAP - Success >> -- Could NOT find Boost >> -- Looking for include file execinfo.h >> -- Looking for include file execinfo.h - not found. >> -- INFO: Rabema not build because zlib was not found. >> CMake Error at core/apps/rabema/CMakeLists.txt:43 (install): >> install TARGETS given target "rabema_build_gold_standard" which does not >> exist in this directory. >>=20 >> -- Boost not found, not building snp_store. >> -- Configuring incomplete, errors occurred! >> PS C:\Seqan\build> >> PS C:\Seqan\build> >>=20 >> How would you fix these errors? I don't have Zlib or BZip2 (do I need >> to download these libraries?). I have Boost (which was not found - do >> I need to specify its path somewhere?). I have Python (which was >> found). >>=20 >> Thanks and I look forward to finding some SeqAn performance issues. >>=20 >> Neil >>=20 >>=20 >> ------------------------------ >>=20 >> _______________________________________________ >> seqan-dev mailing list >> seqan-dev@lists.fu-berlin.de >> https://lists.fu-berlin.de/listinfo/seqan-dev >>=20 >>=20 >> End of seqan-dev Digest, Vol 32, Issue 8 >> **************************************** >=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 From Jochen.Singer@fu-berlin.de Thu May 31 09:52:54 2012 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 <1Sa0Bg-0006NW-Ec>; Thu, 31 May 2012 09:52:52 +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 <1Sa0Bg-00012I-Bk>; Thu, 31 May 2012 09:52:52 +0200 Received: from cas1.campus.fu-berlin.de ([130.133.170.201]) by relay2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Sa0Bg-00049v-5r>; Thu, 31 May 2012 09:52:52 +0200 Received: from EX01B.campus.fu-berlin.de ([130.133.170.131]) by CAS1.campus.fu-berlin.de ([130.133.170.201]) with mapi id 14.02.0298.004; Thu, 31 May 2012 09:52:51 +0200 From: "Singer, Jochen" To: SeqAn Development Thread-Topic: [Seqan-dev] seqan-dev Digest, Vol 32, Issue 8 Thread-Index: AQHNPuOSx3fMBAj2jUG5O7WOOD+aC5bjU00AgAARDgCAAAEVgA== Date: Thu, 31 May 2012 07:52:49 +0000 Message-ID: <3E8C4A6F-3C7E-4EAE-8F9E-2FAFDAABA335@campus.fu-berlin.de> References: , <0A95298C-87A4-436C-8CC0-B4D7B76A9D6A@campus.fu-berlin.de> In-Reply-To: <0A95298C-87A4-436C-8CC0-B4D7B76A9D6A@campus.fu-berlin.de> Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: text/plain; charset="iso-8859-1" Content-ID: <4D414312CF49E64C85C19767ABBE4FA8@campus.fu-berlin.de> Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Originating-IP: 130.133.170.201 X-purgate: suspect X-purgate-type: suspect X-purgate-ID: 151147::1338450772-00000D73-861627B3/3588765268-0/0-1 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] seqan-dev Digest, Vol 32, Issue 8 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, 31 May 2012 07:52:54 -0000 Hi all, sorry for my stupidity. Just ignore the last mail! Sorry for the inconvenience, Jochen On 31.05.2012, at 09:48, Singer, Jochen wrote: > Hi Manuel, >=20 > ich wollte dich nur fragen, ob ihr mir bescheid sagen k=F6nnte, wenn ihr = euch f=FCr code entscheidet, da ich so auch sehe, welche teile sensibel sin= d :-) >=20 > On 31.05.2012, at 08:47, Holtgrewe, Manuel wrote: >=20 >> Hi Neal, sorry for providing the HTTPS link. The correct link is: >>=20 >> http://trac.seqan.de/wiki/HowTo/InstallContribsWindows >>=20 >> The SeqAn Trac is publically available via HTTP. >>=20 >> I'll send another email about performance sensitive code later after a d= iscussion with colleagues. >>=20 >> Cheers, >> Manuel >> ________________________________________ >> From: Neil Justice [njjustice@gmail.com] >> Sent: Thursday, May 31, 2012 6:12 AM >> To: seqan-dev@lists.fu-berlin.de >> Subject: Re: [Seqan-dev] seqan-dev Digest, Vol 32, Issue 8 >>=20 >> Thanks Manuel. Your fix to that CMakeLists.txt file allowed me to run >> CMake without error and generate an .sln file. >>=20 >> The code now builds for me except for these four compiler errors: >>=20 >> error C3861: 'Bam': identifier not >> found c:\Seqan\seqan-trunk\extras\demos\bam_library_size.cpp 244 >> error C2665: 'open' : none of the 8 overloads could convert all the >> argument types c:\Seqan\seqan-trunk\extras\demos\bam_library_size.cpp = 238 >> error C2079: 'inBamStream' uses undefined class >> 'seqan::Stream' c:\Seqan\seqan-trunk\extras\demos\bam_library_size.cpp = 237 >> error C2065: 'Bgzf' : undeclared >> identifier c:\Seqan\seqan-trunk\extras\demos\bam_library_size.cpp = 237 >>=20 >> How are these errors resolved? >>=20 >> Assuming these errors are resolved by obtaining zlib/bzlib: link >> https://trac.seqan.de/wiki/HowTo/InstallContribsWindows leads to a >> login/password prompt for FU Berlin for which I have no login or >> password. Is there another link to zlib/bzlib? >>=20 >> Also, which files contain the most performance-sensitive code? >>=20 >> Cheers, >> Neil >>=20 >> On Tue, May 29, 2012 at 5:00 AM, = wrote: >>> Send seqan-dev mailing list submissions to >>> seqan-dev@lists.fu-berlin.de >>>=20 >>> To subscribe or unsubscribe via the World Wide Web, visit >>> https://lists.fu-berlin.de/listinfo/seqan-dev >>> or, via email, send a message with subject or body 'help' to >>> seqan-dev-request@lists.fu-berlin.de >>>=20 >>> You can reach the person managing the list at >>> seqan-dev-owner@lists.fu-berlin.de >>>=20 >>> When replying, please edit your Subject line so it is more specific >>> than "Re: Contents of seqan-dev digest..." >>>=20 >>>=20 >>> Today's Topics: >>>=20 >>> 1. Re: I'm interested in making SeqAn faster but am stopped by >>> these CMake errors (Holtgrewe, Manuel) >>>=20 >>>=20 >>> ---------------------------------------------------------------------- >>>=20 >>> Message: 1 >>> Date: Mon, 28 May 2012 10:14:43 +0000 >>> From: "Holtgrewe, Manuel" >>> To: SeqAn Development >>> Subject: Re: [Seqan-dev] I'm interested in making SeqAn faster but am >>> stopped by these CMake errors >>> Message-ID: >>> >>> Content-Type: text/plain; charset=3D"us-ascii" >>>=20 >>> Dear Neil, >>>=20 >>> the problem is caused by a bug in one of the CMakeLists.txt files. This= should be corrected now. >>>=20 >>> As for zlib/bzlib, you can simply install prebuilt versions of these li= braries: >>>=20 >>> https://trac.seqan.de/wiki/HowTo/InstallContribsWindows >>>=20 >>> Most of the library will also work without zlib, but for reading BAM fi= les or compressed streams, you will need it. This is also explained in some= detail in some messages after the configuration. >>>=20 >>> Cheers, >>> Manuel >>> ________________________________________ >>> From: Neil Justice [njjustice@gmail.com] >>> Sent: Monday, May 28, 2012 2:32 AM >>> To: seqan-dev@lists.fu-berlin.de >>> Subject: [Seqan-dev] I'm interested in making SeqAn faster but am stopp= ed by these CMake errors >>>=20 >>> Hello SeqAn developers, >>>=20 >>> My name is Neil Justice and I'm interested in helping advance genetics >>> research by contributing my programming skills to the task of making >>> SeqAn faster. I work on performance tuning the C++ of a high-frequency >>> algorithmic trading program at a hedge fund in Houston. Lately I've >>> been interested in finding an interesting and good-for-humanity open >>> source project to work on at home, and SeqAn appears to be that >>> project. >>>=20 >>> I am on Windows and am trying to generate a Visual Studio 2008 .sln >>> for SeqAn using CMake. I've pulled the code using svn per tutorial >>> http://trac.seqan.de/wiki/Tutorial/GettingStarted. Here are the CMake >>> errors I encounter in response to CMake command "cmake >>> C:\Seqan\seqan-trunk -G "Visual Studio 9 2008"" (errors also attached >>> as a screenshot): >>>=20 >>> PS C:\Seqan\build> cmake C:\Seqan\seqan-trunk -G "Visual Studio 9 2008" >>> -- Check for working C compiler using: Visual Studio 9 2008 >>> -- Check for working C compiler using: Visual Studio 9 2008 -- works >>> -- Detecting C compiler ABI info >>> -- Detecting C compiler ABI info - done >>> -- Check for working CXX compiler using: Visual Studio 9 2008 >>> -- Check for working CXX compiler using: Visual Studio 9 2008 -- works >>> -- Detecting CXX compiler ABI info >>> -- Detecting CXX compiler ABI info - done >>> SEQAN_CONTRIB_BASE is undefined! >>> -- CMAKE_FIND_ROOT_PATH is "". >>> -- Found PythonInterp: C:/Python32/python.exe (found version "3.2.3") >>> -- Zlib could not be found! >>> -- BZip2 libraries could not be found! >>> -- Try OpenMP C flag =3D [/openmp] >>> -- Performing Test OpenMP_FLAG_DETECTED >>> -- Performing Test OpenMP_FLAG_DETECTED - Success >>> -- Try OpenMP CXX flag =3D [/openmp] >>> -- Performing Test OpenMP_FLAG_DETECTED >>> -- Performing Test OpenMP_FLAG_DETECTED - Success >>> -- Performing Test TR1_SHARED_PTR_USE_TR1_MEMORY >>> -- Performing Test TR1_SHARED_PTR_USE_TR1_MEMORY - Failed >>> -- Performing Test TR1_SHARED_PTR_USE_MEMORY >>> -- Performing Test TR1_SHARED_PTR_USE_MEMORY - Success >>> -- Performing Test TR1_UNORDERED_MAP_USE_TR1_UNORDERED_MAP >>> -- Performing Test TR1_UNORDERED_MAP_USE_TR1_UNORDERED_MAP - Failed >>> -- Performing Test TR1_UNORDERED_MAP_USE_UNORDERED_MAP >>> -- Performing Test TR1_UNORDERED_MAP_USE_UNORDERED_MAP - Success >>> -- Could NOT find Boost >>> -- Looking for include file execinfo.h >>> -- Looking for include file execinfo.h - not found. >>> -- INFO: Rabema not build because zlib was not found. >>> CMake Error at core/apps/rabema/CMakeLists.txt:43 (install): >>> install TARGETS given target "rabema_build_gold_standard" which does no= t >>> exist in this directory. >>>=20 >>> -- Boost not found, not building snp_store. >>> -- Configuring incomplete, errors occurred! >>> PS C:\Seqan\build> >>> PS C:\Seqan\build> >>>=20 >>> How would you fix these errors? I don't have Zlib or BZip2 (do I need >>> to download these libraries?). I have Boost (which was not found - do >>> I need to specify its path somewhere?). I have Python (which was >>> found). >>>=20 >>> Thanks and I look forward to finding some SeqAn performance issues. >>>=20 >>> Neil >>>=20 >>>=20 >>> ------------------------------ >>>=20 >>> _______________________________________________ >>> seqan-dev mailing list >>> seqan-dev@lists.fu-berlin.de >>> https://lists.fu-berlin.de/listinfo/seqan-dev >>>=20 >>>=20 >>> End of seqan-dev Digest, Vol 32, Issue 8 >>> **************************************** >>=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 > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev From kathrin.trappe@fu-berlin.de Thu May 31 09:53:44 2012 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 <1Sa0CV-0006PW-KC>; Thu, 31 May 2012 09:53:43 +0200 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 <1Sa0CV-0001Mb-Gm>; Thu, 31 May 2012 09:53:43 +0200 Received: from celegans.imp.fu-berlin.de ([160.45.111.134]) by inpost2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtpsa (envelope-from ) id <1Sa0CV-0005Ct-Cq>; Thu, 31 May 2012 09:53:43 +0200 Message-ID: <4FC72431.2070802@fu-berlin.de> Date: Thu, 31 May 2012 09:56:33 +0200 From: Kathrin Trappe User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:12.0) Gecko/20120430 Thunderbird/12.0.1 MIME-Version: 1.0 To: SeqAn Development References: , <0A95298C-87A4-436C-8CC0-B4D7B76A9D6A@campus.fu-berlin.de> <3E8C4A6F-3C7E-4EAE-8F9E-2FAFDAABA335@campus.fu-berlin.de> In-Reply-To: <3E8C4A6F-3C7E-4EAE-8F9E-2FAFDAABA335@campus.fu-berlin.de> Content-Type: multipart/mixed; boundary="------------010609090002080006020101" X-Originating-IP: 160.45.111.134 X-purgate: suspect X-purgate-type: suspect X-purgate-ID: 151147::1338450823-00000D73-D974AABC/3588765268-0/0-1 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 Dschibuti.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] seqan-dev Digest, Vol 32, Issue 8 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, 31 May 2012 07:53:44 -0000 This is a multi-part message in MIME format. --------------010609090002080006020101 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit lol :) On 05/31/2012 09:52 AM, Singer, Jochen wrote: > Hi all, > > sorry for my stupidity. Just ignore the last mail! > > Sorry for the inconvenience, > Jochen > > > > On 31.05.2012, at 09:48, Singer, Jochen wrote: > >> Hi Manuel, >> >> ich wollte dich nur fragen, ob ihr mir bescheid sagen könnte, wenn ihr euch für code entscheidet, da ich so auch sehe, welche teile sensibel sind :-) >> >> On 31.05.2012, at 08:47, Holtgrewe, Manuel wrote: >> >>> Hi Neal, sorry for providing the HTTPS link. The correct link is: >>> >>> http://trac.seqan.de/wiki/HowTo/InstallContribsWindows >>> >>> The SeqAn Trac is publically available via HTTP. >>> >>> I'll send another email about performance sensitive code later after a discussion with colleagues. >>> >>> Cheers, >>> Manuel >>> ________________________________________ >>> From: Neil Justice [njjustice@gmail.com] >>> Sent: Thursday, May 31, 2012 6:12 AM >>> To: seqan-dev@lists.fu-berlin.de >>> Subject: Re: [Seqan-dev] seqan-dev Digest, Vol 32, Issue 8 >>> >>> Thanks Manuel. Your fix to that CMakeLists.txt file allowed me to run >>> CMake without error and generate an .sln file. >>> >>> The code now builds for me except for these four compiler errors: >>> >>> error C3861: 'Bam': identifier not >>> found c:\Seqan\seqan-trunk\extras\demos\bam_library_size.cpp 244 >>> error C2665: 'open' : none of the 8 overloads could convert all the >>> argument types c:\Seqan\seqan-trunk\extras\demos\bam_library_size.cpp 238 >>> error C2079: 'inBamStream' uses undefined class >>> 'seqan::Stream' c:\Seqan\seqan-trunk\extras\demos\bam_library_size.cpp 237 >>> error C2065: 'Bgzf' : undeclared >>> identifier c:\Seqan\seqan-trunk\extras\demos\bam_library_size.cpp 237 >>> >>> How are these errors resolved? >>> >>> Assuming these errors are resolved by obtaining zlib/bzlib: link >>> https://trac.seqan.de/wiki/HowTo/InstallContribsWindows leads to a >>> login/password prompt for FU Berlin for which I have no login or >>> password. Is there another link to zlib/bzlib? >>> >>> Also, which files contain the most performance-sensitive code? >>> >>> Cheers, >>> Neil >>> >>> On Tue, May 29, 2012 at 5:00 AM, wrote: >>>> Send seqan-dev mailing list submissions to >>>> seqan-dev@lists.fu-berlin.de >>>> >>>> To subscribe or unsubscribe via the World Wide Web, visit >>>> https://lists.fu-berlin.de/listinfo/seqan-dev >>>> or, via email, send a message with subject or body 'help' to >>>> seqan-dev-request@lists.fu-berlin.de >>>> >>>> You can reach the person managing the list at >>>> seqan-dev-owner@lists.fu-berlin.de >>>> >>>> When replying, please edit your Subject line so it is more specific >>>> than "Re: Contents of seqan-dev digest..." >>>> >>>> >>>> Today's Topics: >>>> >>>> 1. Re: I'm interested in making SeqAn faster but am stopped by >>>> these CMake errors (Holtgrewe, Manuel) >>>> >>>> >>>> ---------------------------------------------------------------------- >>>> >>>> Message: 1 >>>> Date: Mon, 28 May 2012 10:14:43 +0000 >>>> From: "Holtgrewe, Manuel" >>>> To: SeqAn Development >>>> Subject: Re: [Seqan-dev] I'm interested in making SeqAn faster but am >>>> stopped by these CMake errors >>>> Message-ID: >>>> >>>> Content-Type: text/plain; charset="us-ascii" >>>> >>>> Dear Neil, >>>> >>>> the problem is caused by a bug in one of the CMakeLists.txt files. This should be corrected now. >>>> >>>> As for zlib/bzlib, you can simply install prebuilt versions of these libraries: >>>> >>>> https://trac.seqan.de/wiki/HowTo/InstallContribsWindows >>>> >>>> Most of the library will also work without zlib, but for reading BAM files or compressed streams, you will need it. This is also explained in some detail in some messages after the configuration. >>>> >>>> Cheers, >>>> Manuel >>>> ________________________________________ >>>> From: Neil Justice [njjustice@gmail.com] >>>> Sent: Monday, May 28, 2012 2:32 AM >>>> To: seqan-dev@lists.fu-berlin.de >>>> Subject: [Seqan-dev] I'm interested in making SeqAn faster but am stopped by these CMake errors >>>> >>>> Hello SeqAn developers, >>>> >>>> My name is Neil Justice and I'm interested in helping advance genetics >>>> research by contributing my programming skills to the task of making >>>> SeqAn faster. I work on performance tuning the C++ of a high-frequency >>>> algorithmic trading program at a hedge fund in Houston. Lately I've >>>> been interested in finding an interesting and good-for-humanity open >>>> source project to work on at home, and SeqAn appears to be that >>>> project. >>>> >>>> I am on Windows and am trying to generate a Visual Studio 2008 .sln >>>> for SeqAn using CMake. I've pulled the code using svn per tutorial >>>> http://trac.seqan.de/wiki/Tutorial/GettingStarted. Here are the CMake >>>> errors I encounter in response to CMake command "cmake >>>> C:\Seqan\seqan-trunk -G "Visual Studio 9 2008"" (errors also attached >>>> as a screenshot): >>>> >>>> PS C:\Seqan\build> cmake C:\Seqan\seqan-trunk -G "Visual Studio 9 2008" >>>> -- Check for working C compiler using: Visual Studio 9 2008 >>>> -- Check for working C compiler using: Visual Studio 9 2008 -- works >>>> -- Detecting C compiler ABI info >>>> -- Detecting C compiler ABI info - done >>>> -- Check for working CXX compiler using: Visual Studio 9 2008 >>>> -- Check for working CXX compiler using: Visual Studio 9 2008 -- works >>>> -- Detecting CXX compiler ABI info >>>> -- Detecting CXX compiler ABI info - done >>>> SEQAN_CONTRIB_BASE is undefined! >>>> -- CMAKE_FIND_ROOT_PATH is "". >>>> -- Found PythonInterp: C:/Python32/python.exe (found version "3.2.3") >>>> -- Zlib could not be found! >>>> -- BZip2 libraries could not be found! >>>> -- Try OpenMP C flag = [/openmp] >>>> -- Performing Test OpenMP_FLAG_DETECTED >>>> -- Performing Test OpenMP_FLAG_DETECTED - Success >>>> -- Try OpenMP CXX flag = [/openmp] >>>> -- Performing Test OpenMP_FLAG_DETECTED >>>> -- Performing Test OpenMP_FLAG_DETECTED - Success >>>> -- Performing Test TR1_SHARED_PTR_USE_TR1_MEMORY >>>> -- Performing Test TR1_SHARED_PTR_USE_TR1_MEMORY - Failed >>>> -- Performing Test TR1_SHARED_PTR_USE_MEMORY >>>> -- Performing Test TR1_SHARED_PTR_USE_MEMORY - Success >>>> -- Performing Test TR1_UNORDERED_MAP_USE_TR1_UNORDERED_MAP >>>> -- Performing Test TR1_UNORDERED_MAP_USE_TR1_UNORDERED_MAP - Failed >>>> -- Performing Test TR1_UNORDERED_MAP_USE_UNORDERED_MAP >>>> -- Performing Test TR1_UNORDERED_MAP_USE_UNORDERED_MAP - Success >>>> -- Could NOT find Boost >>>> -- Looking for include file execinfo.h >>>> -- Looking for include file execinfo.h - not found. >>>> -- INFO: Rabema not build because zlib was not found. >>>> CMake Error at core/apps/rabema/CMakeLists.txt:43 (install): >>>> install TARGETS given target "rabema_build_gold_standard" which does not >>>> exist in this directory. >>>> >>>> -- Boost not found, not building snp_store. >>>> -- Configuring incomplete, errors occurred! >>>> PS C:\Seqan\build> >>>> PS C:\Seqan\build> >>>> >>>> How would you fix these errors? I don't have Zlib or BZip2 (do I need >>>> to download these libraries?). I have Boost (which was not found - do >>>> I need to specify its path somewhere?). I have Python (which was >>>> found). >>>> >>>> Thanks and I look forward to finding some SeqAn performance issues. >>>> >>>> Neil >>>> >>>> >>>> ------------------------------ >>>> >>>> _______________________________________________ >>>> seqan-dev mailing list >>>> seqan-dev@lists.fu-berlin.de >>>> https://lists.fu-berlin.de/listinfo/seqan-dev >>>> >>>> >>>> End of seqan-dev Digest, Vol 32, Issue 8 >>>> **************************************** >>> _______________________________________________ >>> 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 >> >> _______________________________________________ >> 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 --------------010609090002080006020101 Content-Type: text/x-vcard; charset=utf-8; name="kathrin_trappe.vcf" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="kathrin_trappe.vcf" begin:vcard fn:Kathrin Trappe n:Trappe;Kathrin org;quoted-printable:Freie Universit=C3=A4t Berlin;Departement of Informatics adr;quoted-printable;dom:;;Takustra=C3=9Fe 9;Berlin;;14195 email;internet:kathrin.trappe@fu-berlin.de title:Algorithmic Bioinformatics (ABI) version:2.1 end:vcard --------------010609090002080006020101-- From manuel.holtgrewe@fu-berlin.de Thu May 31 13:07:26 2012 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 <1Sa3Dw-0004au-NJ>; Thu, 31 May 2012 13:07:24 +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 <1Sa3Dw-00027p-KB>; Thu, 31 May 2012 13:07:24 +0200 Received: from cas3.campus.fu-berlin.de ([130.133.170.203]) by relay2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Sa3Dw-0000pk-H7>; Thu, 31 May 2012 13:07:24 +0200 Received: from EX02A.campus.fu-berlin.de ([130.133.170.132]) by CAS3.campus.fu-berlin.de ([130.133.170.203]) with mapi id 14.02.0298.004; Thu, 31 May 2012 13:07:23 +0200 From: "Holtgrewe, Manuel" To: SeqAn Development Thread-Topic: [Seqan-dev] seqan-dev Digest, Vol 32, Issue 8 Thread-Index: AQHNPuOSgnRNWAG9MkW/w0un4ZU4w5bjuKUI Date: Thu, 31 May 2012 11:07:22 +0000 Message-ID: References: , In-Reply-To: Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Originating-IP: 130.133.170.203 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1338462444-00000D73-16C49114/0-0/0-0 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: Re: [Seqan-dev] seqan-dev Digest, Vol 32, Issue 8 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, 31 May 2012 11:07:26 -0000 Hi Neal,=0A= =0A= Regarding performance sensitive code: My main assumption here is that you a= re looking for an area to contribute to. Maybe you could elaborate a bit o= n what you want to do. Do you want to look into performance-tweaking parts = of the library or "generally contribute performance-wise" to the library? B= elow, I give some possible projects for both.=0A= =0A= The inner loops are inside the index (most interesting: q-gram, ESA, WOTD i= ndices) and online string search finders (myers and banded myers algorithm = are the most interesting here for edit distance). The index building algori= thms are also a point for possible optimization. Also important to many app= lications is the SWIFT q-gram counting based and pigeonhole filter algorith= ms.=0A= =0A= Another larger area with inner loops are the alignment algorithms but we ar= e in the process of rewriting this part of SeqAn. Hopefully this will be co= mpleted in 1-2 months so it becomes a possible target.=0A= =0A= I am not too sure whether these are low-hanging fruits for performance opti= mization because we looked into this in detail in most cases. That said, if= you are interested in this area, I can give you the exact locations and ex= plain how to write performance test programs with real-world input.=0A= =0A= If I may somewhat widen your question from "performance issues" to "perform= ance-related", it might be easier to find a "big bang for the buck" problem= to tackle. Here, improved implementations or parallelization of certain im= portant library parts come to mind. Some examples:=0A= =0A= - Parallel compression and decompression of BGZF files (they consist of gzi= p compressed blocks and could thus be parallelized). This comes down to por= ting an existing threadpool library to C++11 and using C++11 threads for a = parallel BGZF reader/writer and BAM file sorter. I have the beginning of th= is on my local disk but we could easily make this a github project. This re= quires no prior knowledge in sequence analysis algorithms but expertise in = C++ and parallel programming.=0A= =0A= - Space efficient BWT construction. This basically consists of implementing= an existing algorithm in SeqAn. More information can be found here: https:= //www.mi.fu-berlin.de/w/ABI/SpaceEfficientBWTConstruction. The requirement = on sequence analysis algorithms is probably quite low here and the necessar= y parts could be learned on the fly.=0A= =0A= - Parallelization of suffix array construction. This is a large chunk of wo= rk and would require to rewrite the parallel external memory part of the al= gorithm and probably extend the external memory algorithms and data structu= res part of SeqAn to parallelism.=0A= =0A= Cheers,=0A= Manuel=0A= =0A= PS: A valuable resource for looking SeqAn-related things up besides the Tut= orial is http://docs.seqan.de/seqan/dev2/.=