From manuel.holtgrewe@fu-berlin.de Thu Oct 04 13:57:20 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 <1TJk3L-0013dR-My>; Thu, 04 Oct 2012 13:57:19 +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 <1TJk3L-002TC7-LO>; Thu, 04 Oct 2012 13:57:19 +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 <1TJk3L-002W8Q-GO>; Thu, 04 Oct 2012 13:57:19 +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 14.02.0318.001; Thu, 4 Oct 2012 13:57:18 +0200 From: "Holtgrewe, Manuel" To: SeqAn Development Thread-Topic: [ANN] SeqAn SVN Migration Thread-Index: Ac2aZwBdDPaRm9uNTdasGzmA2j/8PAHwEVKR Date: Thu, 4 Oct 2012 11:57:17 +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::1349351839-0009BEC1-330C06C6/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED X-Spam-Checker-Version: SpamAssassin 3.3.2 on Benin.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] [ANN] SeqAn SVN Migration 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, 04 Oct 2012 11:57:20 -0000 Dear all,=0A= =0A= the migration is complete.=0A= =0A= Please migrate over to the new repository by performing a new checkout of h= ttp://svn.seqan.de/trunk/seqan.=0A= =0A= It is not possible to use svn switch for this.=0A= =0A= Do not hesitate to send an email in the case that you run into problems.=0A= =0A= Sorry for any inconvenience.=0A= =0A= Cheers,=0A= Manuel=0A= ________________________________________=0A= From: Holtgrewe, Manuel [manuel.holtgrewe@fu-berlin.de]=0A= Sent: Monday, September 24, 2012 5:15 PM=0A= To: seqan-dev@lists.fu-berlin.de=0A= Subject: [Seqan-dev] [ANN] SeqAn SVN Migration=0A= =0A= Dear all,=0A= =0A= the URL of the SeqAn repository will change this week from http://svn.mi.fu= -berlin.de/seqan to http://svn.seqan.de/seqan. Furthermore, the hierarchy w= ill move one level up, i.e. from http://svn.mi.fu-berlin.de/seqan/trunk/seq= an to http://svn.seqan.de/seqan/trunk.=0A= =0A= We will freeze the Subversion repository on the current location on Wednesd= ay at 10am Berlin time and begin migrating the library over. After the migr= ation is complete, we will send around a description of how to switch over = to the new repository.=0A= =0A= If you have any questions or remarks then do not hesitate to send them to u= s.=0A= =0A= Cheers,=0A= Manuel=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 Fri Oct 05 16:36:45 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 <1TK91A-001sZM-QG>; Fri, 05 Oct 2012 16:36:44 +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 <1TK91A-002bN2-OH>; Fri, 05 Oct 2012 16:36:44 +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 <1TK91A-000GmZ-Iq>; Fri, 05 Oct 2012 16:36:44 +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 14.02.0318.001; Fri, 5 Oct 2012 16:36:43 +0200 From: "Holtgrewe, Manuel" To: SeqAn Development Thread-Topic: [ANN] SeqAn SVN Migration Thread-Index: Ac2aZwBdDPaRm9uNTdasGzmA2j/8PAHwEVKRADfeIM0= Date: Fri, 5 Oct 2012 14:36:42 +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::1349447804-0009BEC1-393759A5/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED X-Spam-Checker-Version: SpamAssassin 3.3.2 on Algerien.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] [ANN] SeqAn SVN Migration 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, 05 Oct 2012 14:36:45 -0000 Sorry, there was a mistake in my email. The true locations is http://svn.se= qan.de/seqan/trunk (I accidently mixed up the last two path components).=0A= ________________________________________=0A= From: Holtgrewe, Manuel [manuel.holtgrewe@fu-berlin.de]=0A= Sent: Thursday, October 04, 2012 1:57 PM=0A= To: SeqAn Development=0A= Subject: Re: [Seqan-dev] [ANN] SeqAn SVN Migration=0A= =0A= Dear all,=0A= =0A= the migration is complete.=0A= =0A= Please migrate over to the new repository by performing a new checkout of h= ttp://svn.seqan.de/trunk/seqan.=0A= =0A= It is not possible to use svn switch for this.=0A= =0A= Do not hesitate to send an email in the case that you run into problems.=0A= =0A= Sorry for any inconvenience.=0A= =0A= Cheers,=0A= Manuel=0A= ________________________________________=0A= From: Holtgrewe, Manuel [manuel.holtgrewe@fu-berlin.de]=0A= Sent: Monday, September 24, 2012 5:15 PM=0A= To: seqan-dev@lists.fu-berlin.de=0A= Subject: [Seqan-dev] [ANN] SeqAn SVN Migration=0A= =0A= Dear all,=0A= =0A= the URL of the SeqAn repository will change this week from http://svn.mi.fu= -berlin.de/seqan to http://svn.seqan.de/seqan. Furthermore, the hierarchy w= ill move one level up, i.e. from http://svn.mi.fu-berlin.de/seqan/trunk/seq= an to http://svn.seqan.de/seqan/trunk.=0A= =0A= We will freeze the Subversion repository on the current location on Wednesd= ay at 10am Berlin time and begin migrating the library over. After the migr= ation is complete, we will send around a description of how to switch over = to the new repository.=0A= =0A= If you have any questions or remarks then do not hesitate to send them to u= s.=0A= =0A= Cheers,=0A= Manuel=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= seqan-dev mailing list=0A= seqan-dev@lists.fu-berlin.de=0A= https://lists.fu-berlin.de/listinfo/seqan-dev=0A= From okko73313@gmail.com Tue Oct 16 18:52:42 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 <1TOANk-003WAU-Ui>; Tue, 16 Oct 2012 18:52:41 +0200 Received: from mail-qc0-f182.google.com ([209.85.216.182]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1TOANk-000355-P5>; Tue, 16 Oct 2012 18:52:40 +0200 Received: by mail-qc0-f182.google.com with SMTP id l39so6458194qcs.13 for ; Tue, 16 Oct 2012 09:52:38 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:reply-to:sender:date:x-google-sender-auth:message-id :subject:from:to:content-type; bh=9qPoEDu/tZM8plu6btVkQXoVOr/+RZWBNsT2vu3VWkY=; b=XM3LTMVv/RldL1FO9K2OYBIoNbxuF++AfN8aAqmX2s1egAS0kV3gb03h3jPsy7py/n qsZLy+C9nQoiaDE/nvA8mhhkLcfkJMaPwMOhHYqYwZJYVnsVZTr581XEv/fOQAHKSX4q 8MK6pNJdztQNwTWmtxB9/RqpL/sss0OpDUsB953Vph0euYKdzFElT+CHHwQlDXdOo/g0 oORlvOYKkhOvHkI80vIdjAKdBJfEU/1kUf58aV1sK+sEIa7M4YryzYsRpigO17nD42jX Dv6UauOtAwNR1ELFiDTWANWCLNGi8kV8QhEcLrcqfuRplTcPx9Iedv3jiGhr46DIch4g UMig== MIME-Version: 1.0 Received: by 10.224.44.135 with SMTP id a7mr27284750qaf.84.1350406358563; Tue, 16 Oct 2012 09:52:38 -0700 (PDT) Sender: okko73313@gmail.com Received: by 10.49.24.72 with HTTP; Tue, 16 Oct 2012 09:52:38 -0700 (PDT) Date: Tue, 16 Oct 2012 18:52:38 +0200 X-Google-Sender-Auth: YsjrkGRin_Q5TrxUuTpd3Qf1Np0 Message-ID: From: Konstantin Okonechnikov To: seqan-dev@lists.fu-berlin.de Content-Type: multipart/mixed; boundary=20cf3074b9204dfb0f04cc2ffbe8 X-Originating-IP: 209.85.216.182 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1350406360-0000097C-D6E36F7E/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=-0.7 required=5.0 tests=FREEMAIL_FROM, FSL_FREEMAIL_1, FSL_FREEMAIL_2,HTML_MESSAGE,RCVD_IN_DNSWL_LOW,T_DKIM_INVALID X-Spam-Checker-Version: SpamAssassin 3.3.2 on Dschibuti.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] check for errors when reading GTF annotations X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 Precedence: list Reply-To: k.okonechnikov@gmail.com, SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 16 Oct 2012 16:52:42 -0000 --20cf3074b9204dfb0f04cc2ffbe8 Content-Type: multipart/alternative; boundary=20cf3074b9204dfb0804cc2ffbe6 --20cf3074b9204dfb0804cc2ffbe6 Content-Type: text/plain; charset=ISO-8859-1 Hi all, How can I check for errors when reading a GTF file? I tried checking return value of read() function, but it doesn't compile (see example attached) Env: Ubuntu Linux 12.04 64bit, GCC 4.6.3 Seqan SVN revision: 13076 Tnx in advance, Konstantin --20cf3074b9204dfb0804cc2ffbe6 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi all,

How can I check for errors when reading a GTF file?

I= tried checking return value of read() function, but it doesn't compile= (see example attached)

Env: Ubuntu Linux 12.04 64bit, GCC 4.6.3
Seqan SVN revision: 13076

Tnx in advance,
=A0=A0 Konstantin
--20cf3074b9204dfb0804cc2ffbe6-- --20cf3074b9204dfb0f04cc2ffbe8 Content-Type: text/x-c++src; charset=US-ASCII; name="test_gtf.cpp" Content-Disposition: attachment; filename="test_gtf.cpp" Content-Transfer-Encoding: base64 X-Attachment-Id: f_h8d8y5sz1 I2luY2x1ZGUgPGNhc3NlcnQ+CiNpbmNsdWRlIDxpb3N0cmVhbT4KCiNpbmNsdWRlIDxzZXFhbi9z dG9yZS5oPgojaW5jbHVkZSA8c2VxYW4vZmlsZS5oPgoKCnVzaW5nIG5hbWVzcGFjZSBzZXFhbjsK CmludCBtYWluKGludCBhcmdjLCBjaGFyIGNvbnN0ICoqIGFyZ3YpCnsKICAgIEZyYWdtZW50U3Rv cmU8PiBzdG9yZTsKICAgICBzdGQ6Omlmc3RyZWFtIGZpbGUoInRlc3QuZ3RmIiwgc3RkOjppb3Nf YmFzZTo6aW4gfCBzdGQ6Omlvc19iYXNlOjpiaW5hcnkpOwoKICAgIC8vIFJlYWQgYW5ub3RhdGlv bnMgZnJvbSB0aGUgR1RGIGZpbGUKICAgIGJvb2wgcmVzID0gcmVhZChmaWxlLCBzdG9yZSwgR3Rm KCkpOwogICAgCiAgICBhc3NlcnQocmVzID09IHRydWUpOwoKCiAgICByZXR1cm4gMDsKfQoKCgoK CgoKCgoKCgo= --20cf3074b9204dfb0f04cc2ffbe8-- From okko73313@gmail.com Thu Oct 18 11:36:55 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 <1TOmX8-003WcK-Fp>; Thu, 18 Oct 2012 11:36:54 +0200 Received: from mail-qa0-f54.google.com ([209.85.216.54]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1TOmX8-000LEW-Ae>; Thu, 18 Oct 2012 11:36:54 +0200 Received: by mail-qa0-f54.google.com with SMTP id p27so1258189qat.13 for ; Thu, 18 Oct 2012 02:36:52 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:reply-to:sender:in-reply-to:references:date :x-google-sender-auth:message-id:subject:from:to:content-type; bh=D+Qr9bs86oqvqLGOA/jd4OWLZPPjMEVYn5xg0EUDdGI=; b=JpIGHmw5PhXTo3GEolillGX0xTTKtSU1Ranp+MoOpGf9YdHTcpnbkA6oH+HrNO77X2 GkthjRahMJITAzkyvf6AyY0iHYxAve+cPX+m1hRFc9h4pA6NhmNGlY3mwJam1k+uFL6b hl8ewLnDerFwz9ET4HbOK2Le4OUQb290DXiE1Uc6k3r1q3EV+H7fbv1deFdDdG5J3UrL ZENbo8HKdb+Xny60qlWHWknoYqwk1P+SuJc/6c9sCV6v2ZiIwSKN4jiLkm/xnsgoytvZ mDsiz4IfEKjd+8HawnR1FZvYlUrkrX/nNtqbyYRTcFsQLYHSmLdVJfl4pBnCB2OFnevI Nvqg== MIME-Version: 1.0 Received: by 10.224.178.4 with SMTP id bk4mr34198839qab.38.1350553012150; Thu, 18 Oct 2012 02:36:52 -0700 (PDT) Sender: okko73313@gmail.com Received: by 10.49.24.72 with HTTP; Thu, 18 Oct 2012 02:36:52 -0700 (PDT) In-Reply-To: References: Date: Thu, 18 Oct 2012 11:36:52 +0200 X-Google-Sender-Auth: qMKMKanL0uU4EpNJ4H5BGXeZ0Jg Message-ID: From: Konstantin Okonechnikov To: seqan-dev@lists.fu-berlin.de Content-Type: multipart/alternative; boundary=20cf302ef94a8a1fc504cc5220b4 X-Originating-IP: 209.85.216.54 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1350553014-0000097C-2CBB8C64/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=-0.7 required=5.0 tests=FREEMAIL_FROM, FSL_FREEMAIL_1, FSL_FREEMAIL_2,HTML_MESSAGE,RCVD_IN_DNSWL_LOW,T_DKIM_INVALID X-Spam-Checker-Version: SpamAssassin 3.3.2 on Burundi.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] check for errors when reading GTF annotations X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 Precedence: list Reply-To: k.okonechnikov@gmail.com, SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 18 Oct 2012 09:36:55 -0000 --20cf302ef94a8a1fc504cc5220b4 Content-Type: text/plain; charset=ISO-8859-1 Hi all, it's me again. Well, according to function signature to read annotations template inline void read ( TFile & file, FragmentStore & fragStore, Gtf) the return type is void, which I also could've guessed from the compilation output. However, I was misleaded by the following documentation page which indicates that return value should be bool: http://docs.seqan.de/seqan/dev/FUNCTION.read.html So, the question remains: how can I check for errors when reading a GTF file? Thanks in advance, Konstantin On Tue, Oct 16, 2012 at 6:52 PM, Konstantin Okonechnikov < k.okonechnikov@gmail.com> wrote: > Hi all, > > How can I check for errors when reading a GTF file? > > I tried checking return value of read() function, but it doesn't compile > (see example attached) > > Env: Ubuntu Linux 12.04 64bit, GCC 4.6.3 > Seqan SVN revision: 13076 > > Tnx in advance, > Konstantin > --20cf302ef94a8a1fc504cc5220b4 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi all,
it's me again.

Well, according to function signature = to read annotations

template<typename TFile, typename TSpec, type= name TConfig>
inline void
read (
=A0=A0=A0 TFile & file,=A0=A0=A0 FragmentStore<TSpec, TConfig> & fragStore,
=A0=A0=A0 Gtf)

the return type is void, which I also could've gu= essed from the compilation output.

However, I was misleaded by the = following documentation page which indicates that return value should be bo= ol:
http://docs.s= eqan.de/seqan/dev/FUNCTION.read.html

So, the question remains: h= ow can I check for errors when reading a GTF file?

Thanks in advance= ,
=A0Konstantin

On Tue, Oct 16, 2012 at 6:5= 2 PM, Konstantin Okonechnikov <k.okonechnikov@gmail.com> wrote:
Hi all,

How can I check for errors wh= en reading a GTF file?

I tried checking return value of read() funct= ion, but it doesn't compile (see example attached)

Env: Ubuntu Linux 12.04 64bit, GCC 4.6.3
Seqan SVN revision: 13076

Tnx in advance,
=A0=A0 Konstantin

--20cf302ef94a8a1fc504cc5220b4-- From okko73313@gmail.com Mon Oct 22 18:59:02 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 <1TQLLB-002Jje-C4>; Mon, 22 Oct 2012 18:59:01 +0200 Received: from mail-qa0-f47.google.com ([209.85.216.47]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1TQLLB-002D1A-2v>; Mon, 22 Oct 2012 18:59:01 +0200 Received: by mail-qa0-f47.google.com with SMTP id i29so1577173qaf.13 for ; Mon, 22 Oct 2012 09:58:59 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:reply-to:sender:in-reply-to:references:date :x-google-sender-auth:message-id:subject:from:to:content-type; bh=BCTIXizGQZomT2mWaALjvJzCq27dJybMokgBolyoKSw=; b=drHTe7t70NluNZLuOMe7XRd5mqUTofCvVFKHRDXMr8Mtb6Py0C7K9sPyOaCRohBGNk QrPDpUN3z+ssAtNaYFs34OKE1pzq71RiBFM5JhlWIKMLuE2vkSV1ynNjS/L9oFIVk4PJ I/PBc8K6luAdk8XLi6GW9NsTof4xKjexbjdn6O6x+jHJOqWM5OcjQIbSNRNVQE8a6aQP TSWfHYCCAQeHeu1hnjv+vwRuh/hCj/wMQz/dGUWSYVS1jmVJFM50QaL6WJeYTaIkUHGQ aHktZsCROjhQhKOwZ5U7IjL1lmy9IvZhGwL0zIqoTtyOuntWayIvkMHivAFlndynvpdz Jw7Q== MIME-Version: 1.0 Received: by 10.224.179.197 with SMTP id br5mr4380775qab.34.1350925138920; Mon, 22 Oct 2012 09:58:58 -0700 (PDT) Sender: okko73313@gmail.com Received: by 10.49.24.72 with HTTP; Mon, 22 Oct 2012 09:58:58 -0700 (PDT) In-Reply-To: References: Date: Mon, 22 Oct 2012 18:58:58 +0200 X-Google-Sender-Auth: g5yw41HqSsSArNg-4fKSj4o6V8w Message-ID: From: Konstantin Okonechnikov To: seqan-dev@lists.fu-berlin.de Content-Type: multipart/mixed; boundary=20cf303b3a9f0603d304cca8c5e5 X-Originating-IP: 209.85.216.47 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1350925141-0000097C-D04786B7/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=-0.7 required=5.0 tests=FREEMAIL_FROM, FSL_FREEMAIL_1, FSL_FREEMAIL_2,HTML_MESSAGE,RCVD_IN_DNSWL_LOW,T_DKIM_INVALID X-Spam-Checker-Version: SpamAssassin 3.3.2 on Dschibuti.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] check for errors when reading GTF annotations X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 Precedence: list Reply-To: k.okonechnikov@gmail.com, SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 22 Oct 2012 16:59:02 -0000 --20cf303b3a9f0603d304cca8c5e5 Content-Type: multipart/alternative; boundary=20cf303b3a9f0603ce04cca8c5e3 --20cf303b3a9f0603ce04cca8c5e3 Content-Type: text/plain; charset=ISO-8859-1 Hi all, Plz find a patch attached. It provides 2 minor improvements for store_io_gff.h: - made checking for simple open file error when loading a GTF file available from read(...) interface - empty strings are now skipped (instead of creating an empty annotation) -- Konstantin On Thu, Oct 18, 2012 at 11:36 AM, Konstantin Okonechnikov < k.okonechnikov@gmail.com> wrote: > Hi all, > it's me again. > > Well, according to function signature to read annotations > > template > inline void > read ( > TFile & file, > FragmentStore & fragStore, > Gtf) > > the return type is void, which I also could've guessed from the > compilation output. > > However, I was misleaded by the following documentation page which > indicates that return value should be bool: > http://docs.seqan.de/seqan/dev/FUNCTION.read.html > > So, the question remains: how can I check for errors when reading a GTF > file? > > Thanks in advance, > Konstantin > > > On Tue, Oct 16, 2012 at 6:52 PM, Konstantin Okonechnikov < > k.okonechnikov@gmail.com> wrote: > >> Hi all, >> >> How can I check for errors when reading a GTF file? >> >> I tried checking return value of read() function, but it doesn't compile >> (see example attached) >> >> Env: Ubuntu Linux 12.04 64bit, GCC 4.6.3 >> Seqan SVN revision: 13076 >> >> Tnx in advance, >> Konstantin >> > > --20cf303b3a9f0603ce04cca8c5e3 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi all,

Plz find a patch attached.

It provides 2 minor impro= vements for store_io_gff.h:
- made checking for simple open file error w= hen loading a GTF file available from read(...) interface
- empty string= s=A0 are now skipped (instead of creating an empty annotation)

--
=A0Konstantin

On Thu, Oct 18, 2= 012 at 11:36 AM, Konstantin Okonechnikov <k.okonechnikov@gmail.com<= /a>> wrote:
Hi all,
it's me again.

Well, a= ccording to function signature to read annotations

template<typen= ame TFile, typename TSpec, typename TConfig>
inline void
read (
=A0=A0=A0 TFile & file,
=A0=A0=A0 Fragment= Store<TSpec, TConfig> & fragStore,
=A0=A0=A0 Gtf)

the return type is void, which I also could've gu= essed from the compilation output.

However, I was misleaded by the = following documentation page which indicates that return value should be bo= ol:
http://docs.seqan.de/seqan/dev/FUNCTION.read.html

So, the q= uestion remains: how can I check for errors when reading a GTF file?
Thanks in advance,
=A0Konstantin


On Tue, Oct 16, 2012 at 6:52 PM, Konstantin Okonechnikov <k.okonechnikov@gmail.com> wrote:
Hi all,

How can I check for errors wh= en reading a GTF file?

I tried checking return value of read() funct= ion, but it doesn't compile (see example attached)

Env: Ubuntu Linux 12.04 64bit, GCC 4.6.3
Seqan SVN revision: 13076

Tnx in advance,
=A0=A0 Konstantin


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I'm using seqan mason to generate mate pairs reads: ./build/Release/core/apps/mason/mason illumina -i -s $i -N 10000000 -n 50 -mp -hM 8 -hnN -o ./reads.fa ./fake_patient.fasta I do not need the sam file as output, is there any way of avoiding that is generated? ( I didn't find any option...) I need high coverage, therefore the 10 million reads. This is taking a lot of time and memory (50 minutes and up to 30Gb), is there a reason for this to take so much memory? am I doing something wrong? (my fasta file is 2.9Gb). Thank you for your help, -- Sonia Vivas From manuel.holtgrewe@fu-berlin.de Wed Oct 24 18:45:04 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 <1TR44l-0031V9-LH>; Wed, 24 Oct 2012 18:45:03 +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 <1TR44l-002lLo-Jg>; Wed, 24 Oct 2012 18:45:03 +0200 Received: from cas2.campus.fu-berlin.de ([130.133.170.202]) by relay2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1TR44l-003VL2-8g>; Wed, 24 Oct 2012 18:45:03 +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 14.02.0318.004; Wed, 24 Oct 2012 18:45:02 +0200 From: "Holtgrewe, Manuel" To: SeqAn Development Thread-Topic: [Seqan-dev] question about mason Thread-Index: AQHNsfnfZaFvDXYOpkCpZgY7IG0x2pfIqXQP Message-ID: References: <50880501.70200@molecularhealth.com> In-Reply-To: <50880501.70200@molecularhealth.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: Wed, 24 Oct 2012 18:45:01 +0200 X-Original-Date: Wed, 24 Oct 2012 16:45:01 +0000 X-Originating-IP: 130.133.170.202 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1351097103-0000097C-E382FD65/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.001695, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED X-Spam-Checker-Version: SpamAssassin 3.3.2 on Burundi.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] question about mason 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, 24 Oct 2012 16:45:05 -0000 Dear Sonia, with the RNG seeds parameter, you can start multiple mason proc= esses (e.g. in parallel) resulting in different, but reproduceable, FASTA f= iles. Generating packages of fewer reads should decrease the running time, = even when run sequentially.=0A= =0A= Currently there is no option to not generate the SAM file. We are working o= n a solution to this.=0A= =0A= HTH,=0A= Manuel=0A= ________________________________________=0A= From: Sonia Vivas [vivas@molecularhealth.com]=0A= Sent: Wednesday, October 24, 2012 5:10 PM=0A= To: seqan-dev@lists.fu-berlin.de=0A= Subject: [Seqan-dev] question about mason=0A= =0A= Hi!=0A= I'm using seqan mason to generate mate pairs reads:=0A= =0A= ./build/Release/core/apps/mason/mason illumina -i -s $i -N 10000000 -n=0A= 50 -mp -hM 8 -hnN -o ./reads.fa ./fake_patient.fasta=0A= =0A= I do not need the sam file as output, is there any way of avoiding that=0A= is generated? ( I didn't find any option...)=0A= I need high coverage, therefore the 10 million reads. This is taking a=0A= lot of time and memory (50 minutes and up to 30Gb), is there a reason=0A= for this to take so much memory? am I doing something wrong? (my fasta=0A= file is 2.9Gb).=0A= =0A= Thank you for your help,=0A= =0A= --=0A= Sonia Vivas=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=