From peter.robinson@charite.de Mon Apr 01 13:09:07 2013 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UMcbq-000zKQ-Jh>; Mon, 01 Apr 2013 13:09:06 +0200 Received: from mail2.charite.de ([141.42.206.200]) by relay1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UMcbq-001h71-Hw>; Mon, 01 Apr 2013 13:09:06 +0200 Received: from localhost (localhost [127.0.0.1]) by mail2.charite.de (Postfix) with ESMTP id 3ZfW5Y2HxczBrPM for ; Mon, 1 Apr 2013 13:09:05 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=charite.de; h= mime-version:content-transfer-encoding:content-type:content-type :content-language:accept-language:message-id:subject:subject :date:date:from:from:received:received:received; s=default; t= 1364814545; x=1366628946; bh=4xzFqZvhZle5Eb/4Hw2JG+6mQSo6IhaEN6Z BFmEYgJ0=; b=I08IUm6p+M4YfcrpNJGRDbnEK2saxbegQhJjBxteS2qjIQra2AI vv2188cBPy5Sye5aWqV+hyuvtP+5txAf0Oi8tShy7TB6dbGIaDm79u2+kutP4i8q 0/M1OHeIX5ItCwE23OP7O/zgssIc2W9UBOlRptMKDJVMMJU3eRwOr+UA= Received: from exchange.charite.de (unknown [10.32.37.106]) (using TLSv1 with cipher AES128-SHA (128/128 bits)) (No client certificate requested) by mail2.charite.de (Postfix) with ESMTPS for ; Mon, 1 Apr 2013 13:09:04 +0200 (CEST) Received: from S-MX-HT1.charite.de (10.32.32.94) by s-mx14-ht02.charite.de (10.32.37.106) with Microsoft SMTP Server (TLS) id 14.2.342.3; Mon, 1 Apr 2013 13:09:03 +0200 Received: from Exchange41.charite.de ([fe80::11de:7e2f:4013:43d7]) by S-MX-HT1.charite.de ([::1]) with mapi; Mon, 1 Apr 2013 13:09:03 +0200 From: "Robinson, Peter" To: "seqan-dev@lists.fu-berlin.de" Date: Mon, 1 Apr 2013 13:09:01 +0200 Thread-Topic: Makefiles Thread-Index: AQHOLslQ5CyT/PWZ3E6/QXi95YQ2/w== Message-ID: Accept-Language: de-DE Content-Language: de-DE X-MS-Has-Attach: X-MS-TNEF-Correlator: acceptlanguage: de-DE Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Originating-IP: 141.42.206.200 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1364814546-00000A3F-76B0B1C1/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=-5.0 required=5.0 tests=RCVD_IN_DNSWL_HI, T_DKIM_INVALID X-Spam-Checker-Version: SpamAssassin 3.3.3-zedat692e3bd7 on Gabun.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] Makefiles 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, 01 Apr 2013 11:09:07 -0000 Hallo! I have a suggestion for the tutorial page here: http://trac.seqan.de/wiki/BuildManual/IntegrationWithYourOwnBuildSystem These flags are recommended: Linux/GCC flags: -lrt (required) -W -Wall -Wno-long-long -pedantic -Wno-var= iadic-macros (optional).=20 However, you should put somewhere that for some seqan functions you also ne= ed the -lz flag (I noticed this with the Record reader, although I am not e= ntirely sure why this is needed to read one uncompressed FASTA file). -thanks & greetings! -Peter Nick. Dr. med. Peter N. Robinson, MSc. Professor of Medical Genomics Institut f=FCr Medizinische Genetik und Humangenetik Charit=E9 - Universit=E4tsmedizin Berlin Augustenburger Platz 1 13353 Berlin Germany +4930 450566006 Mobile: 0160 93769872 peter.robinson@charite.de http://compbio.charite.de http://www.human-phenotype-ontology.org Introduction to Bio-Ontologies: http://www.crcpress.com/product/isbn/978143= 9836651 To give your data to the bioinformatician after the experiment is done may = be no more than asking him to perform a post-mortem examination: he may be = able to say what the experiment died of. ~ after Sir Ronald Aylmer Fisher= From manuel.holtgrewe@fu-berlin.de Mon Apr 01 23:18:50 2013 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UMm7t-001n1y-RE>; Mon, 01 Apr 2013 23:18:49 +0200 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UMm7t-001OIt-PQ>; Mon, 01 Apr 2013 23:18:49 +0200 Received: from cas2.campus.fu-berlin.de ([130.133.170.202]) by relay2.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UMm7t-001Mai-AP>; Mon, 01 Apr 2013 23:18:49 +0200 Received: from EX02A.campus.fu-berlin.de ([130.133.170.132]) by CAS2.campus.fu-berlin.de ([130.133.170.202]) with mapi id 14.03.0123.003; Mon, 1 Apr 2013 23:18:48 +0200 From: "Holtgrewe, Manuel" To: SeqAn Development Thread-Topic: Makefiles Thread-Index: AQHOLslQ5CyT/PWZ3E6/QXi95YQ2/5jB30dK 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="iso-8859-1" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 Date: Mon, 01 Apr 2013 23:18:46 +0200 X-Original-Date: Mon, 1 Apr 2013 21:18:46 +0000 X-Originating-IP: 130.133.170.202 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1364851129-00000A3F-BF116BBA/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=-50.0 required=5.0 tests=ALL_TRUSTED X-Spam-Checker-Version: SpamAssassin 3.3.3-zedat692e3bd7 on Botsuana.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] Makefiles 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, 01 Apr 2013 21:18:50 -0000 Hi Nick, I've just added a note to the description on the site to the SEQAN= _HAS_ZLIB compiler define.=0A= ________________________________________=0A= From: Robinson, Peter [peter.robinson@charite.de]=0A= Sent: Monday, April 01, 2013 1:09 PM=0A= To: seqan-dev@lists.fu-berlin.de=0A= Subject: [Seqan-dev] Makefiles=0A= =0A= Hallo!=0A= =0A= I have a suggestion for the tutorial page here:=0A= =0A= http://trac.seqan.de/wiki/BuildManual/IntegrationWithYourOwnBuildSystem=0A= =0A= These flags are recommended:=0A= =0A= Linux/GCC flags: -lrt (required) -W -Wall -Wno-long-long -pedantic -Wno-var= iadic-macros (optional).=0A= =0A= =0A= However, you should put somewhere that for some seqan functions you also ne= ed the -lz flag (I noticed this with the Record reader, although I am not e= ntirely sure why this is needed to read one uncompressed FASTA file).=0A= =0A= -thanks & greetings!=0A= -Peter Nick.=0A= =0A= =0A= =0A= Dr. med. Peter N. Robinson, MSc.=0A= Professor of Medical Genomics=0A= Institut f=FCr Medizinische Genetik und Humangenetik=0A= Charit=E9 - Universit=E4tsmedizin Berlin=0A= Augustenburger Platz 1=0A= 13353 Berlin=0A= Germany=0A= +4930 450566006=0A= Mobile: 0160 93769872=0A= peter.robinson@charite.de=0A= http://compbio.charite.de=0A= http://www.human-phenotype-ontology.org=0A= Introduction to Bio-Ontologies: http://www.crcpress.com/product/isbn/978143= 9836651=0A= =0A= To give your data to the bioinformatician after the experiment is done may = be no more than asking him to perform a post-mortem examination: he may be = able to say what the experiment died of.=0A= ~ after Sir Ronald Aylmer Fisher=0A= _______________________________________________=0A= seqan-dev mailing list=0A= seqan-dev@lists.fu-berlin.de=0A= https://lists.fu-berlin.de/listinfo/seqan-dev=0A= From s.henderson@ucl.ac.uk Mon Apr 22 17:43:22 2013 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UUItl-001hds-IO>; Mon, 22 Apr 2013 17:43:21 +0200 Received: from am1ehsobe005.messaging.microsoft.com ([213.199.154.208] helo=am1outboundpool.messaging.microsoft.com) by relay1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UUItl-002QiT-CW>; Mon, 22 Apr 2013 17:43:21 +0200 Received: from mail101-am1-R.bigfish.com (10.3.201.253) by AM1EHSOBE015.bigfish.com (10.3.207.137) with Microsoft SMTP Server id 14.1.225.23; Mon, 22 Apr 2013 15:43:18 +0000 Received: from mail101-am1 (localhost [127.0.0.1]) by mail101-am1-R.bigfish.com (Postfix) with ESMTP id 787B3C0313 for ; Mon, 22 Apr 2013 15:43:18 +0000 (UTC) X-Forefront-Antispam-Report: CIP:157.56.250.117; KIP:(null); UIP:(null); IPV:NLI; H:AMXPRD0111HT002.eurprd01.prod.exchangelabs.com; RD:none; EFVD:NLI X-SpamScore: 3 X-BigFish: PS3(zcb8kzc85dhzz1f42h1fc6h1ee6h1de0h1d18h1fdah1202h1e76h1d1ah1d2ahzz18c673hz2dh2a8h668h839hd25hf0ah1288h12a5h12bdh137ah1441h1504h1537h153bh15d0h162dh1631h1758h18e1h1946h19b5h19ceh1ad9h1b0ah1bceh1155h) Received: from mail101-am1 (localhost.localdomain [127.0.0.1]) by mail101-am1 (MessageSwitch) id 1366645396304170_31259; Mon, 22 Apr 2013 15:43:16 +0000 (UTC) Received: from AM1EHSMHS002.bigfish.com (unknown [10.3.201.251]) by mail101-am1.bigfish.com (Postfix) with ESMTP id 475A43E0066 for ; Mon, 22 Apr 2013 15:43:16 +0000 (UTC) Received: from AMXPRD0111HT002.eurprd01.prod.exchangelabs.com (157.56.250.117) by AM1EHSMHS002.bigfish.com (10.3.207.102) with Microsoft SMTP Server (TLS) id 14.1.225.23; Mon, 22 Apr 2013 15:43:13 +0000 Received: from AMXPRD0111MB472.eurprd01.prod.exchangelabs.com ([169.254.10.240]) by AMXPRD0111HT002.eurprd01.prod.exchangelabs.com ([10.242.12.163]) with mapi id 14.16.0293.001; Mon, 22 Apr 2013 15:43:13 +0000 From: "Henderson, Stephen" To: "seqan-dev@lists.fu-berlin.de" Thread-Topic: Dna5Q - how do you access qual or seq ? Thread-Index: AQHOP3AYT5xICuac4EqK4ljNYWSnjw== Date: Mon, 22 Apr 2013 15:43:12 +0000 Message-ID: <98456EB61783264C9A843890618267F84FEDAD38@AMXPRD0111MB472.eurprd01.prod.exchangelabs.com> Accept-Language: en-GB, en-US Content-Language: en-GB X-MS-Has-Attach: X-MS-TNEF-Correlator: x-ucllive-sclrule: HASRUN Content-Type: multipart/alternative; boundary="_000_98456EB61783264C9A843890618267F84FEDAD38AMXPRD0111MB472_" MIME-Version: 1.0 X-OriginatorOrg: ucl.ac.uk X-Originating-IP: 213.199.154.208 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1366645401-00000A3F-6FFD8D76/0-0/0-0 X-Bogosity: Unsure, tests=bogofilter, spamicity=0.460459, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=0.8 required=5.0 tests=FU_BOGO_UNSURE,HTML_MESSAGE, RCVD_IN_DNSWL_LOW X-Spam-Checker-Version: SpamAssassin 3.3.3-zedat692e3bd7 on Gabun.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] Dna5Q - how do you access qual or seq ? 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, 22 Apr 2013 15:43:22 -0000 --_000_98456EB61783264C9A843890618267F84FEDAD38AMXPRD0111MB472_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello I am enjoying using your excellent seqan tools. I have a couple of queries = too though. Partly as a learning exercise I have been trying to use seqan to re-create = a version of the fastqc software accessed from R - which I pass summary dat= a for graphics and trivial stats. I'm using the double pass-reader to minimise memory of fastq - which works = nicely for a minimal speed penalty (nice). So I can do most of what I want = using the longer version of quality reads.. ... seqan::StringSet ids; seqan::StringSet seqs; // a Charstring seqan::StringSet quals; if (read2(ids, seqs, quals, reader, seqan::Fastq()) !=3D 0) etc... However it strikes me that it would be preferable to be able to use the Dna= 5Q Stringset and half the code and runtime: ... seqan::StringSet ids; seqan::StringSet seqsQ; // Dna5Q if (read2(ids, seqsQ, reader, seqan::Fastq()) !=3D 0) etc... This because I would prefer for efficiency (i.e not double passing) and cod= e legibility (laziness???) to iterate a single loop through a StringSet seq= sQ for QC calculations. However I cannot see how to obtain the quality valu= e from the score. The tutorial material and the documentation I can find su= ggests to me that this should be possible though I cannot find an actual ex= ample... ordValue I find works for qual CharString but is not overloaded for Dna5Q. = Nor does getQualityValue seem to work as I think it is described in the doc= umentation... //where seqs is the StringSet of Dna5Q read in above seqan::Dna5Q seq=3D seqs[0]; Rcpp::Rcout << getQualityValue(seq[0]) << std::endl; // error Rcpp::Rcout << (int)(ordValue(seq[0]) - 33) << std::endl; //error So ... sorry for the lengthy post but how do I access the qualities?... or = indeed the sequences of the Dna5Q when I have read in both? I realise this is probably a trivial syntactic error but it has stumped me = for a couple of days now. Thanks Stephen Henderson UCL Cancer Institute --_000_98456EB61783264C9A843890618267F84FEDAD38AMXPRD0111MB472_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hello
I am enjoying using your excellent seqan tools. I have a couple of que= ries too though.

Partly as a learning exercise I have been trying to use seqan to re-cr= eate a version of the fastqc software accessed from R - which I pass summar= y data for graphics and trivial stats.

I'm using the double pass-reader to minimise memory of fastq - which w= orks nicely for a minimal speed penalty (nice). So I can do most of what I = want using the longer version of quality reads..

...=
seq= an::StringSet<seqan::CharString> ids;
seq= an::StringSet<seqan::CharString> seqs; // a Charstring
seq= an::StringSet<seqan::CharString> quals;
if = (read2(ids, seqs, quals, reader, seqan::Fastq()) !=3D 0)
etc= ...

However it strikes me that it would be preferable to be able to use th= e Dna5Q Stringset and half the code and runtime:
...=
seq= an::StringSet<seqan::CharString> ids;
seq= an::StringSet<seqan::Dna5Q> seqsQ; // Dna5Q
if = (read2(ids, seqsQ, reader, seqan::Fastq()) !=3D 0)
etc= ...

This because I would prefer for efficiency (i.e not double passing) an= d code legibility (laziness???) to iterate a single loop through a StringSe= t seqsQ for QC calculations. However I cannot see how to obtain t= he quality value from the score. The tutorial material and the documentatio= n I can find suggests to me that this should be possible though I cannot fi= nd an actual example... 

ordValue I find works for qual CharString but is not overloaded for Dn= a5Q. Nor does getQualityValue seem to work as I think it is described in th= e documentation...

//w= here seqs is the StringSet of Dna5Q read in above
seq= an::Dna5Q seq=3D seqs[0];

Rcp= p::Rcout << getQualityValue(seq[0]) << std::endl;    = // error
Rcp= p::Rcout << (int)(ordValue(seq[0]) - 33) << std::endl= ;    //error


So ... sorry for the lengthy post but how do I access the qualities?..= . or indeed the sequences of the Dna5Q when I have read in both? 

I realise this is probably a trivial syntactic error but it has stumpe= d me for a couple of days now.

Thanks
Stephen Henderson
UCL Cancer Institute



--_000_98456EB61783264C9A843890618267F84FEDAD38AMXPRD0111MB472_-- From lkuchenb@inf.fu-berlin.de Mon Apr 22 18:25:32 2013 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UUJYZ-001knG-9a>; Mon, 22 Apr 2013 18:25:31 +0200 Received: from europe.unique-internet.de ([188.40.122.211]) by relay1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UUJYZ-002eNw-5N>; Mon, 22 Apr 2013 18:25:31 +0200 Received: from localhost (localhost [127.0.0.1]) by europe.unique-internet.de (Postfix) with ESMTP id 02936A5A002 for ; Mon, 22 Apr 2013 18:25:30 +0200 (CEST) Received: from europe.unique-internet.de ([127.0.0.1]) by localhost (europe.unique-internet.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id dRqj9CmyD5+A for ; Mon, 22 Apr 2013 18:25:29 +0200 (CEST) Received: from prolin.imp.fu-berlin.de (prolin.imp.fu-berlin.de [160.45.111.85]) by europe.unique-internet.de (Postfix) with ESMTPSA id B4FE0A5A001 for ; Mon, 22 Apr 2013 18:25:29 +0200 (CEST) Message-ID: <51756472.40802@inf.fu-berlin.de> Date: Mon, 22 Apr 2013 18:25:22 +0200 From: Leon Kuchenbecker User-Agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:17.0) Gecko/20130328 Thunderbird/17.0.5 MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de References: <98456EB61783264C9A843890618267F84FEDAD38@AMXPRD0111MB472.eurprd01.prod.exchangelabs.com> In-Reply-To: <98456EB61783264C9A843890618267F84FEDAD38@AMXPRD0111MB472.eurprd01.prod.exchangelabs.com> X-Enigmail-Version: 1.5.1 Content-Type: multipart/signed; protocol="application/pkcs7-signature"; micalg=sha1; boundary="------------ms020105050507000200030103" X-Originating-IP: 188.40.122.211 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1366647931-00000A3F-C487C6FF/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.010416, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=0.0 required=5.0 tests=none X-Spam-Checker-Version: SpamAssassin 3.3.3-zedat692e3bd7 on Benin.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] Dna5Q - how do you access qual or seq ? 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, 22 Apr 2013 16:25:32 -0000 This is a cryptographically signed message in MIME format. --------------ms020105050507000200030103 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi Stephen! > //where seqs is the StringSet of Dna5Q read in above > seqan::Dna5Q seq=3D seqs[0]; >=20 > Rcpp::Rcout << getQualityValue(seq[0]) << std::endl; // error > [...] seqan::Dna5Q is a type for storing a single character from the ACGTN alphabet including the associated quality. If you want to store a sequence of such characters, you need String. Thus, the correct types for your variables would be > seqan::StringSet ids; > seqan::StringSet > seqsQ; Your usage of getQualityValue() was in principle correct, just that you were trying to subscript a single character. Cheers Leon --=20 You can use my PGP pubkey (0x010E29F5) to encrypt mail addressed to me () ascii ribbon campaign - against html e-mail /\ www.asciiribbon.org - against proprietary attachments --------------ms020105050507000200030103 Content-Type: application/pkcs7-signature; name="smime.p7s" Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="smime.p7s" Content-Description: S/MIME Cryptographic Signature MIAGCSqGSIb3DQEHAqCAMIACAQExCzAJBgUrDgMCGgUAMIAGCSqGSIb3DQEHAQAAoIINkzCC BjQwggQcoAMCAQICASAwDQYJKoZIhvcNAQEFBQAwfTELMAkGA1UEBhMCSUwxFjAUBgNVBAoT DVN0YXJ0Q29tIEx0ZC4xKzApBgNVBAsTIlNlY3VyZSBEaWdpdGFsIENlcnRpZmljYXRlIFNp Z25pbmcxKTAnBgNVBAMTIFN0YXJ0Q29tIENlcnRpZmljYXRpb24gQXV0aG9yaXR5MB4XDTA3 MTAyNDIxMDI1NVoXDTE3MTAyNDIxMDI1NVowgYwxCzAJBgNVBAYTAklMMRYwFAYDVQQKEw1T dGFydENvbSBMdGQuMSswKQYDVQQLEyJTZWN1cmUgRGlnaXRhbCBDZXJ0aWZpY2F0ZSBTaWdu aW5nMTgwNgYDVQQDEy9TdGFydENvbSBDbGFzcyAyIFByaW1hcnkgSW50ZXJtZWRpYXRlIENs 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([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UUbPU-003jdf-3s>; Tue, 23 Apr 2013 13:29:20 +0200 Received: from co1ehsobe002.messaging.microsoft.com ([216.32.180.185] helo=co1outboundpool.messaging.microsoft.com) by relay1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UUbPT-003czC-Mx>; Tue, 23 Apr 2013 13:29:20 +0200 Received: from mail15-co1-R.bigfish.com (10.243.78.232) by CO1EHSOBE020.bigfish.com (10.243.66.83) with Microsoft SMTP Server id 14.1.225.23; Tue, 23 Apr 2013 11:29:16 +0000 Received: from mail15-co1 (localhost [127.0.0.1]) by mail15-co1-R.bigfish.com (Postfix) with ESMTP id 1B1C52C02B2 for ; Tue, 23 Apr 2013 11:29:16 +0000 (UTC) X-Forefront-Antispam-Report: CIP:157.56.250.117; KIP:(null); UIP:(null); IPV:NLI; H:AMXPRD0111HT003.eurprd01.prod.exchangelabs.com; RD:none; EFVD:NLI X-SpamScore: 1 X-BigFish: PS1(zcb8kz1432I111aIzz1f42h1fc6h1ee6h1de0h1d18h1fdah1202h1e76h1d1ah1d2ahzzz2dh2a8h668h839h944hd25hf0ah1220h1288h12a5h12a9h12bdh137ah13b6h1441h1504h1537h153bh15d0h162dh1631h1758h18e1h1946h19b5h19ceh1ad9h1b0ah1155h) Received: from mail15-co1 (localhost.localdomain [127.0.0.1]) by mail15-co1 (MessageSwitch) id 1366716553632112_13878; Tue, 23 Apr 2013 11:29:13 +0000 (UTC) Received: from CO1EHSMHS016.bigfish.com (unknown [10.243.78.244]) by mail15-co1.bigfish.com (Postfix) with ESMTP id 9824CC8008C for ; Tue, 23 Apr 2013 11:29:13 +0000 (UTC) Received: from AMXPRD0111HT003.eurprd01.prod.exchangelabs.com (157.56.250.117) by CO1EHSMHS016.bigfish.com (10.243.66.26) with Microsoft SMTP Server (TLS) id 14.1.225.23; Tue, 23 Apr 2013 11:29:13 +0000 Received: from AMXPRD0111MB472.eurprd01.prod.exchangelabs.com ([169.254.10.240]) by AMXPRD0111HT003.eurprd01.prod.exchangelabs.com ([10.242.12.164]) with mapi id 14.16.0293.001; Tue, 23 Apr 2013 11:28:52 +0000 From: "Henderson, Stephen" To: "seqan-dev@lists.fu-berlin.de" Thread-Topic: Re: Dna5Q - how do you access qual or seq ? (Leon Kuchenbecker) Thread-Index: AQHOQBS3hud16rHJA0qT+JNXrHQKTA== Date: Tue, 23 Apr 2013 11:28:51 +0000 Message-ID: <98456EB61783264C9A843890618267F84FEDC1A9@AMXPRD0111MB472.eurprd01.prod.exchangelabs.com> Accept-Language: en-GB, en-US Content-Language: en-GB X-MS-Has-Attach: X-MS-TNEF-Correlator: x-ucllive-sclrule: HASRUN Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-OriginatorOrg: ucl.ac.uk X-Originating-IP: 216.32.180.185 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1366716560-00000A3F-9FED37C9/0-0/0-0 X-Bogosity: Unsure, tests=bogofilter, spamicity=0.499065, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=0.8 required=5.0 tests=FU_BOGO_UNSURE, RCVD_IN_DNSWL_LOW X-Spam-Checker-Version: SpamAssassin 3.3.3-zedat692e3bd7 on Gabun.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] Dna5Q - how do you access qual or seq ? (Leon Kuchenbecker) 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, 23 Apr 2013 11:29:21 -0000 Thanks=0A= =0A= That is exactly the sort of syntactic headslap I imagined (doh!). Cheers. = =0A= =0A= While I'm here just out of curiosity do you know =0A= =0A= a) The size in RAM a fastq file takes up when single pass read vs double pa= ss (~ per million 75mers)? =0A= =0A= b) Does Dna5Q and the alternative of a seqs, qual charstring take up the s= ame space in RAM? =0A= =0A= c) Is there any extra overhead in iterating or extracting elements from Dna= 5Q as opposed to a simple charstring?=0A= =0A= d) Is Dna5Q something like a Vector of ???=0A= =0A= =0A= ... anyway thanks again.=0A= Stephen=0A= =0A= =0A= =0A= =0A= -----------------------=0A= Hi Stephen!=0A= =0A= > //where seqs is the StringSet of Dna5Q read in above=0A= > seqan::Dna5Q seq=3D seqs[0];=0A= >=0A= > Rcpp::Rcout << getQualityValue(seq[0]) << std::endl; // error=0A= > [...]=0A= =0A= seqan::Dna5Q is a type for storing a single character from the ACGTN=0A= alphabet including the associated quality. If you want to store a=0A= sequence of such characters, you need String.=0A= =0A= Thus, the correct types for your variables would be=0A= =0A= > seqan::StringSet ids;=0A= > seqan::StringSet > seqsQ;=0A= =0A= Your usage of getQualityValue() was in principle correct, just that you=0A= were trying to subscript a single character.=0A= =0A= Cheers=0A= Leon=0A= =0A= =0A= =0A= From manuel.holtgrewe@fu-berlin.de Tue Apr 23 13:58:02 2013 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UUbrF-003lmb-5V>; Tue, 23 Apr 2013 13:58:01 +0200 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UUbrF-003RZA-3j>; Tue, 23 Apr 2013 13:58:01 +0200 Received: from cas3.campus.fu-berlin.de ([130.133.170.203]) by relay2.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UUbrE-001b5L-Ro>; Tue, 23 Apr 2013 13:58:01 +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 14.03.0123.003; Tue, 23 Apr 2013 13:57:58 +0200 From: "Holtgrewe, Manuel" To: SeqAn Development Thread-Topic: [Seqan-dev] Dna5Q - how do you access qual or seq ? (Leon Kuchenbecker) Thread-Index: AQHOQBS3hud16rHJA0qT+JNXrHQKTJjjsU7l Message-ID: References: <98456EB61783264C9A843890618267F84FEDC1A9@AMXPRD0111MB472.eurprd01.prod.exchangelabs.com> In-Reply-To: <98456EB61783264C9A843890618267F84FEDC1A9@AMXPRD0111MB472.eurprd01.prod.exchangelabs.com> 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 Date: Tue, 23 Apr 2013 13:57:57 +0200 X-Original-Date: Tue, 23 Apr 2013 11:57:57 +0000 X-Originating-IP: 130.133.170.203 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1366718281-00000A3F-1890ED0F/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.371391, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=-50.0 required=5.0 tests=ALL_TRUSTED X-Spam-Checker-Version: SpamAssassin 3.3.3-zedat692e3bd7 on Dschibuti.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] Dna5Q - how do you access qual or seq ? (Leon Kuchenbecker) 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, 23 Apr 2013 11:58:02 -0000 Hi Stephen,=0A= =0A= a) If you read with double pass I/O (I recommend to ONLY use MMap String fo= r double-pass I/O because of memory usage for buffering), and read into a C= oncatDirect StringSet then the memory usage should be 1 byte per Dna5Q incl= uding char and memory.=0A= =0A= b) Dna5Q uses one byte, if you store the sequence and qualities separately,= you one byte for each the char and one byte for the quality, thus twice th= e amount of memory. Note that your input file have to use PHRED scores.=0A= =0A= c) There is a small overhead (bitmasks, bit shifts, lookup tables) for retr= ieving the character/quality from a Dna5Q character, but if you iterate seq= uentially over the data, using Dna5Q will most probably be faster since you= only need to transfer 1/2 of the data from main memory to registers.=0A= =0A= d) Not exactly. Dna5Q is one character, String is a string of Dna5Q = characters. DnaQ (not Dna5Q) stores the character in the first two bits and= the quality in the remaining bits. Each alphabet entry can have qualities = 0..62. For Dna5Q, the story is a bit more complicated since N automatically= implies a quality of 0, thus the pair analogy is broken here.=0A= =0A= HTH,=0A= Manuel=0A= =0A= ________________________________________=0A= From: Henderson, Stephen [s.henderson@ucl.ac.uk]=0A= Sent: Tuesday, April 23, 2013 1:28 PM=0A= To: seqan-dev@lists.fu-berlin.de=0A= Subject: Re: [Seqan-dev] Dna5Q - how do you access qual or seq ? (Leon Kuc= henbecker)=0A= =0A= Thanks=0A= =0A= That is exactly the sort of syntactic headslap I imagined (doh!). Cheers.= =0A= =0A= While I'm here just out of curiosity do you know=0A= =0A= a) The size in RAM a fastq file takes up when single pass read vs double pa= ss (~ per million 75mers)?=0A= =0A= b) Does Dna5Q and the alternative of a seqs, qual charstring take up the s= ame space in RAM?=0A= =0A= c) Is there any extra overhead in iterating or extracting elements from Dna= 5Q as opposed to a simple charstring?=0A= =0A= d) Is Dna5Q something like a Vector of ???=0A= =0A= =0A= ... anyway thanks again.=0A= Stephen=0A= =0A= =0A= =0A= =0A= -----------------------=0A= Hi Stephen!=0A= =0A= > //where seqs is the StringSet of Dna5Q read in above=0A= > seqan::Dna5Q seq=3D seqs[0];=0A= >=0A= > Rcpp::Rcout << getQualityValue(seq[0]) << std::endl; // error=0A= > [...]=0A= =0A= seqan::Dna5Q is a type for storing a single character from the ACGTN=0A= alphabet including the associated quality. If you want to store a=0A= sequence of such characters, you need String.=0A= =0A= Thus, the correct types for your variables would be=0A= =0A= > seqan::StringSet ids;=0A= > seqan::StringSet > seqsQ;=0A= =0A= Your usage of getQualityValue() was in principle correct, just that you=0A= were trying to subscript a single character.=0A= =0A= Cheers=0A= Leon=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= From manuel.holtgrewe@fu-berlin.de Tue Apr 23 17:07:32 2013 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UUeod-0045rU-5S>; Tue, 23 Apr 2013 17:07:31 +0200 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UUeod-000oDg-3v>; Tue, 23 Apr 2013 17:07:31 +0200 Received: from cas2.campus.fu-berlin.de ([130.133.170.202]) by relay2.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UUeoc-002RZf-Rd>; Tue, 23 Apr 2013 17:07:31 +0200 Received: from EX02A.campus.fu-berlin.de ([130.133.170.132]) by CAS2.campus.fu-berlin.de ([130.133.170.202]) with mapi id 14.03.0123.003; Tue, 23 Apr 2013 17:07:25 +0200 From: "Holtgrewe, Manuel" To: "seqan-dev@lists.fu-berlin.de" Thread-Topic: Recent Renamings Thread-Index: Ac5AMicoOi/fwx4lSQGWpPa/aWzqlA== Message-ID: 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 Date: Tue, 23 Apr 2013 17:07:24 +0200 X-Original-Date: Tue, 23 Apr 2013 15:07:24 +0000 X-Originating-IP: 130.133.170.202 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1366729651-00000A3F-F980F49D/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=-50.0 required=5.0 tests=ALL_TRUSTED X-Spam-Checker-Version: SpamAssassin 3.3.3-zedat692e3bd7 on Dschibuti.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] Recent Renamings 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, 23 Apr 2013 15:07:32 -0000 Dear all,=0A= =0A= I just wanted to let you know that in our preparations of the 1.4 release, = we are doing some renaming for better consistency. Since the functionality = is not present in the 1.3 release, you will not read about them in the 1.4 = changelog.=0A= =0A= BamAlignmentRecord::rId =3D> BamAlignmentRecord::rID=0A= BamAlignmentRecord::pos =3D> BamAlignmentRecord::beginPos=0A= GffRecord::seqIdx =3D> GffRecord::rID=0A= GffRecord::seqID =3D> GffRecord::ref=0A= =0A= Also see [1].=0A= =0A= Furthermore:=0A= =0A= RecordReader > =3D> RecordReader >=0A= RecordReader > =3D> RecordReader >=0A= =0A= We're sorry for all caused inconveniences.=0A= =0A= Cheers,=0A= Manuel=0A= =0A= [1] https://trac.seqan.de/ticket/1006= From weese@campus.fu-berlin.de Mon Apr 29 17:44:48 2013 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UWqFz-003wYf-NN>; Mon, 29 Apr 2013 17:44:47 +0200 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UWqFz-000E9K-Lr>; Mon, 29 Apr 2013 17:44:47 +0200 Received: from cas3.campus.fu-berlin.de ([130.133.170.203]) by relay2.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UWqFz-001JYY-Av>; Mon, 29 Apr 2013 17:44:47 +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 14.03.0123.003; Mon, 29 Apr 2013 17:44:46 +0200 From: "Weese, David" To: "seqan-dev@lists.fu-berlin.de" Thread-Topic: New SeqAn Version 1.4 Released Thread-Index: AQHORPB5yEuxGYveeUSVIJIgylf3EQ== Message-ID: <03D75EB8-C3DB-41BE-AEE5-1BF27176CECC@campus.fu-berlin.de> Accept-Language: de-DE, en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: text/plain; charset="Windows-1252" Content-ID: <9D70D11F3C77B44993E0A357473B91D6@campus.fu-berlin.de> Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 Date: Mon, 29 Apr 2013 17:44:45 +0200 X-Original-Date: Mon, 29 Apr 2013 15:44:45 +0000 X-Originating-IP: 130.133.170.203 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1367250287-00000A3F-0EB0D401/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000001, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=-50.0 required=5.0 tests=ALL_TRUSTED X-Spam-Checker-Version: SpamAssassin 3.3.3-zedat9255cc3 on Botsuana.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] New SeqAn Version 1.4 Released 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, 29 Apr 2013 15:44:48 -0000 Hi everyone, The SeqAn team is happy to announce the 1.4 Release of the SeqAn apps and l= ibraries. This update includes all improvements and changes over the last t= wo years since the 1.3 release. You can download the release packages at ht= tp://packages.seqan.de. Some highlights are: =95 New read mapping programs Masai [2] (backtracks two string tries in pa= rallel) and RazerS 3 [3] (uses q-gram index filters and OpenMP). =95 An efficient implementation of an FM index that combines good performa= nce with low memory usage and can be iterated as a prefix trie via the stri= ng tree iterator interface [4]. =95 A new command line parser [5] that facilitates the integration of prog= rams into workflow engines such as KNIME [6] or Galaxy [7]. =95 An extended and more robust I/O system, namely in the modules seq_io, = gff_io, bam_io. You can find a list of many more updates in our Trac wiki in the Changelog = [8]. If you are upgrading from a previous release, you can learn about the new l= ibrary content in the updated tutorial [9]. In case of questions or support, please send an email to our mailing list. Have fun! The SeqAn Team [1] http://packages.seqan.de/ [2] http://www.seqan.de/projects/masai/ [3] http://www.seqan.de/projects/razers/ [4] http://trac.seqan.de/wiki/1.4/Tutorial/IndexIterators [5] http://trac.seqan.de/wiki/1.4/Tutorial/ParsingCommandLineArguments [6] http://www.knime.org/ [7] http://www.galaxyproject.org/ [8] http://trac.seqan.de/wiki/ChangeLog [9] http://trac.seqan.de/wiki/Tutorial [10] https://lists.fu-berlin.de/listinfo/seqan-dev#subscribe= From Birte.Kehr@fu-berlin.de Mon Apr 29 17:51:03 2013 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UWqM1-003wub-SU>; Mon, 29 Apr 2013 17:51:02 +0200 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UWqM1-000H9V-Qd>; Mon, 29 Apr 2013 17:51:01 +0200 Received: from cas2.campus.fu-berlin.de ([130.133.170.202]) by relay2.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UWqM1-001KKG-F3>; Mon, 29 Apr 2013 17:51:01 +0200 Received: from EX01B.campus.fu-berlin.de ([130.133.170.131]) by CAS2.campus.fu-berlin.de ([130.133.170.202]) with mapi id 14.03.0123.003; Mon, 29 Apr 2013 17:51:00 +0200 From: "Kehr, Birte" To: SeqAn Development Thread-Topic: New SeqAn Version 1.4 Released Thread-Index: AQHORPB5yEuxGYveeUSVIJIgylf3EZjtV9/A Message-ID: <20CE9F50DC70454B8C1A480E61365C040DD67D@ex01b.campus.fu-berlin.de> References: <03D75EB8-C3DB-41BE-AEE5-1BF27176CECC@campus.fu-berlin.de> In-Reply-To: <03D75EB8-C3DB-41BE-AEE5-1BF27176CECC@campus.fu-berlin.de> Accept-Language: de-DE, en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 Date: Mon, 29 Apr 2013 17:50:59 +0200 X-Original-Date: Mon, 29 Apr 2013 15:50:59 +0000 X-Originating-IP: 130.133.170.202 X-purgate: suspect X-purgate-type: suspect X-purgate-ID: 151147::1367250661-00000A3F-5694D709/3862361358-0/0-1 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=-49.0 required=5.0 tests=ALL_TRUSTED, FU_XPURGATE_SUSP X-Spam-Checker-Version: SpamAssassin 3.3.3-zedat9255cc3 on Dschibuti.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] New SeqAn Version 1.4 Released 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, 29 Apr 2013 15:51:03 -0000 Sch=F6n, sch=F6n, Gl=FCckwunsch! Auf seqan.de ist es noch nicht unter Downloads zu finden, wenn man =FCber d= ie linke Men=FCleiste geht. Und ist das Changelog von 1.4 noch Work in Progress oder darf ich den Zusat= z aus der =DCberschrift auf der Trac-Seite entfernen? Gr=FC=DFe, Birte -----Original Message----- From: Weese, David [mailto:weese@campus.fu-berlin.de]=20 Sent: Montag, 29. April 2013 17:45 To: seqan-dev@lists.fu-berlin.de Subject: [Seqan-dev] New SeqAn Version 1.4 Released Hi everyone, The SeqAn team is happy to announce the 1.4 Release of the SeqAn apps and l= ibraries. This update includes all improvements and changes over the last t= wo years since the 1.3 release. You can download the release packages at ht= tp://packages.seqan.de. Some highlights are: . New read mapping programs Masai [2] (backtracks two string tries in para= llel) and RazerS 3 [3] (uses q-gram index filters and OpenMP). . An efficient implementation of an FM index that combines good performanc= e with low memory usage and can be iterated as a prefix trie via the string= tree iterator interface [4]. . A new command line parser [5] that facilitates the integration of progra= ms into workflow engines such as KNIME [6] or Galaxy [7]. . An extended and more robust I/O system, namely in the modules seq_io, gf= f_io, bam_io. You can find a list of many more updates in our Trac wiki in the Changelog = [8]. If you are upgrading from a previous release, you can learn about the new l= ibrary content in the updated tutorial [9]. In case of questions or support, please send an email to our mailing list. Have fun! The SeqAn Team [1] http://packages.seqan.de/ [2] http://www.seqan.de/projects/masai/ [3] http://www.seqan.de/projects/razers/ [4] http://trac.seqan.de/wiki/1.4/Tutorial/IndexIterators [5] http://trac.seqan.de/wiki/1.4/Tutorial/ParsingCommandLineArguments [6] http://www.knime.org/ [7] http://www.galaxyproject.org/ [8] http://trac.seqan.de/wiki/ChangeLog [9] http://trac.seqan.de/wiki/Tutorial [10] https://lists.fu-berlin.de/listinfo/seqan-dev#subscribe _______________________________________________ seqan-dev mailing list seqan-dev@lists.fu-berlin.de https://lists.fu-berlin.de/listinfo/seqan-dev From sebastien.boisvert.3@ulaval.ca Mon Apr 29 19:09:40 2013 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UWra7-0045R7-9P>; Mon, 29 Apr 2013 19:09:39 +0200 Received: from exch-edge02.ulaval.ca ([132.203.244.22]) by relay1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1UWra7-000UpB-3L>; Mon, 29 Apr 2013 19:09:39 +0200 Received: from [192.168.128.130] (132.203.142.18) by EXCH-EDGE02.ulaval.ca (132.203.244.22) with Microsoft SMTP Server id 8.3.298.1; Mon, 29 Apr 2013 13:09:35 -0400 Message-ID: <517EA94F.7080008@ulaval.ca> Date: Mon, 29 Apr 2013 13:09:35 -0400 From: =?windows-1252?Q?S=E9bastien_Boisvert?= User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:17.0) Gecko/20130219 Thunderbird/17.0.3 MIME-Version: 1.0 To: SeqAn Development References: <03D75EB8-C3DB-41BE-AEE5-1BF27176CECC@campus.fu-berlin.de> In-Reply-To: <03D75EB8-C3DB-41BE-AEE5-1BF27176CECC@campus.fu-berlin.de> Content-Type: text/plain; charset="windows-1252"; format=flowed Content-Transfer-Encoding: 8bit X-Originating-IP: 132.203.244.22 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1367255379-00000A3F-00596440/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.040456, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=-5.0 required=5.0 tests=RCVD_IN_DNSWL_HI X-Spam-Checker-Version: SpamAssassin 3.3.3-zedat9255cc3 on Gabun.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] New SeqAn Version 1.4 Released 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, 29 Apr 2013 17:09:40 -0000 Hi David, Nice to hear from you. Congratulation on the annual release of SeqAn. -Sébastien. On 29/04/13 11:44 AM, Weese, David wrote: > Hi everyone, > > The SeqAn team is happy to announce the 1.4 Release of the SeqAn apps and libraries. This update includes all improvements and changes over the last two years since the 1.3 release. You can download the release packages at http://packages.seqan.de. > > Some highlights are: > > • New read mapping programs Masai [2] (backtracks two string tries in parallel) and RazerS 3 [3] (uses q-gram index filters and OpenMP). > • An efficient implementation of an FM index that combines good performance with low memory usage and can be iterated as a prefix trie via the string tree iterator interface [4]. > • A new command line parser [5] that facilitates the integration of programs into workflow engines such as KNIME [6] or Galaxy [7]. > • An extended and more robust I/O system, namely in the modules seq_io, gff_io, bam_io. > > You can find a list of many more updates in our Trac wiki in the Changelog [8]. > If you are upgrading from a previous release, you can learn about the new library content in the updated tutorial [9]. > In case of questions or support, please send an email to our mailing list. > > Have fun! > The SeqAn Team > > > [1] http://packages.seqan.de/ > [2] http://www.seqan.de/projects/masai/ > [3] http://www.seqan.de/projects/razers/ > [4] http://trac.seqan.de/wiki/1.4/Tutorial/IndexIterators > [5] http://trac.seqan.de/wiki/1.4/Tutorial/ParsingCommandLineArguments > [6] http://www.knime.org/ > [7] http://www.galaxyproject.org/ > [8] http://trac.seqan.de/wiki/ChangeLog > [9] http://trac.seqan.de/wiki/Tutorial > [10] https://lists.fu-berlin.de/listinfo/seqan-dev#subscribe > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev >