From manuel.holtgrewe@fu-berlin.de Sun Apr 01 13:32:55 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 <1SEJ1g-0005H1-Uy>; Sun, 01 Apr 2012 13:32:53 +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 <1SEJ1g-0006xl-Sf>; Sun, 01 Apr 2012 13:32:52 +0200 Received: from 91-65-212-104-dynip.superkabel.de ([91.65.212.104] helo=[192.168.0.101]) by inpost2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtpsa (envelope-from ) id <1SEJ1g-0000yu-PI>; Sun, 01 Apr 2012 13:32:52 +0200 Message-ID: <4F783CE4.1050908@fu-berlin.de> Date: Sun, 01 Apr 2012 13:32:52 +0200 From: Manuel Holtgrewe User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:11.0) Gecko/20120310 Thunderbird/11.0 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: 91.65.212.104 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1333279972-000018DE-187F5E08/0-0/0-0 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] Reading FastQ files from GZ archive 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: Sun, 01 Apr 2012 11:32:55 -0000 Dear JD, the DnaQ and Dna5Q alphabets are using PHRED scaled qualities. You should be able to read arbitrary qualities by giving an additional CharString for the qualities to the readRecord function call: // ... RecordReader, SinglePass<> > reader(fastq_file); CharString id; String seq; CharString qual; if (readRecord(id, seq, qual, reader, Fastq()) != 0) return 1; You then have to conver the qualities into PHRED scale manually and assign them to the Dna5Q String seq. Another solution would be to convert the FASTQ files to PHRED scale in a preprocessing step. There currently is not such functionality in SeqAn, but we plan to add this in a later release. The main problem to tackle is how to perform a robust guess about the quality scale -- it is not obvious which scale a FASTQ file is in. HTH Manuel On 03/31/2012 10:35 PM, ngs geek wrote: > I forgot to add an example: > > raw quality string: > bbbeeeeegfggfiiiiiiidgfagdghfdfhdcdfdfb_ca`BOWU^GBBOLGLU_H_Z_BLLLGLLFX]aNWWWY_bb_``BBBBBBBBBBBBBBBBB > > seqan quality string: > ___________________________________________!OWU^G!!OLGLU_H_Z_!LLLGLLFX]_NWWWY______B!BBBBBBBBBBBBBBB > > Best > JD > > On Sat, Mar 31, 2012 at 3:39 PM, ngs geek > wrote: > > Thanks! I'm seeing that the quality string is not the same that I > read from the fastq file. > Are they scaled? I read the doc here > http://trac.seqan.de/wiki/WhitePapers/QualityHandling > but I can't figure out if these are guess by assignQualityValues ... > in any case, I can't see > consistent results for my Illumina 1.3+ reads. > > Thanks > JD > > On Sat, Mar 31, 2012 at 5:22 AM, Holtgrewe, Manuel >

> wrote: > > Hi JD, > > good catch, you found a bug I just fixed. The problem was that > assignQualityValues() did not resize the target string, it does > now. Update your SVN checkout and it should work. > > Also, there now is a demo for reading FASTQ from gzipped files > in core/demos/stream_read_fastq_gz.cpp > > HTH > Manuel > > ------------------------------------------------------------------------ > *From:* ngs geek [ngsgeek@gmail.com ] > *Sent:* Friday, March 30, 2012 7:44 PM > *To:* seqan-dev@lists.fu-berlin.de > > *Subject:* [Seqan-dev] Reading FastQ files from GZ archive > > Hi All: > > I'm trying to filter reads contained in a gz file based on > quality score; I was able to stream the id and the > sequence with GZFile stream and using a singlepass reader (I > don't want to keep the reads in memory). > Unfortunately, I can't access the quality string. > > RecordReader, SinglePass<> > reader(fastq_file); > CharString id; > String seq; > CharString qual; > > while (!atEnd(reader)) > { > if (readRecord(id, seq, reader, Fastq()) != 0) > { > std::cerr << "Problem with your FASTQ file." << std::endl; > return 1; > } > > // reading qual > } > > Any idea on this? I tried assignQualities etc. with no luck. > > Thanks > JD > > > _______________________________________________ > 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 bernd.jagla@pasteur.fr Mon Apr 02 17:16:43 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 <1SEizq-0004aI-CN>; Mon, 02 Apr 2012 17:16:43 +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 <1SEizp-0000iC-Mn>; Mon, 02 Apr 2012 17:16:42 +0200 Received: from maroilles.sis.pasteur.fr (localhost [127.0.0.1]) by mail-interne3.pasteur.fr (Postfix) with ESMTP id B7E383811BA for ; Mon, 2 Apr 2012 14:39:04 +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 771113811AF for ; Mon, 2 Apr 2012 14:39:04 +0200 (CEST) Message-ID: <4F799DEA.1010705@pasteur.fr> Date: Mon, 02 Apr 2012 14:39:06 +0200 From: Bernd Jagla User-Agent: Mozilla/5.0 (Windows NT 5.1; rv:11.0) Gecko/20120327 Thunderbird/11.0.1 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::1333379802-000018DE-02F93260/0-0/0-0 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 X-Spam-Status: No, score=1.4 required=5.0 tests=DNS_FROM_RFC_POST Subject: [Seqan-dev] ModifiedString 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: Mon, 02 Apr 2012 15:16:43 -0000 Hi, I have the following function: bool qualityThreshold(Dna5String& seq1, CharString& qual1, Dna5String& seq2, CharString& qual2, int qualityThreshold, int minLen, bool& pairedEnd, int& countPrimeTrimmed, int& lengthConstrain ) { now, I want to use the reverse sequence as an input using : Dna5StringReverse revSeq1(seq1); I guess I misunderstand something here, but it seems that Dna5StringReverse is not returning a DNA5String but its own type... How can I convert the Reverse in a regular DNA5String? Thanks for the clarification, Bernd From ngsgeek@gmail.com Mon Apr 02 20:34:06 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 <1SEm4p-0001qB-Mb>; Mon, 02 Apr 2012 20:34:03 +0200 Received: from mail-pb0-f54.google.com ([209.85.160.54]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1SEm4p-0005dm-7j>; Mon, 02 Apr 2012 20:34:03 +0200 Received: by pbcwz17 with SMTP id wz17so5113363pbc.13 for ; Mon, 02 Apr 2012 11:34:00 -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; bh=svMzBTqBwuaSa8CjSGowMpVtElxhEXmCpfVTz2VOq1Q=; b=B3h7VdMKth7ZYyjw/IVJgS4ewKddQuztfQLmyx0rOGW6mJFZ4ext1rUFr2Nj5smA8h 8Nq9vbaT1/oAF7t7kQ1FisJfO36Ssbu2Sq8TklWb6sm1Up9BIqBC23j86yBZqYiPqqc9 FcDVEu86709A21vJP/DZOwBKV9RMEIIi+uN/hbNn/ASbX+eUUrPadQkRigCzhZ0pPGrC H/slh3hg7XunHJlqqrj7cCOu2bYQSElkLSqxGUEO9/MMQ6RJ/IhbcR8f+TomvtJ9+hUJ GxZvAwwMai5wPPHEqC/nrExRgdLbWqn2Wze340wqbLxJU1XG+XnlRsiDf42l4FGi8PP+ hVng== MIME-Version: 1.0 Received: by 10.68.213.202 with SMTP id nu10mr22487922pbc.37.1333391640568; Mon, 02 Apr 2012 11:34:00 -0700 (PDT) Received: by 10.66.220.66 with HTTP; Mon, 2 Apr 2012 11:34:00 -0700 (PDT) In-Reply-To: <4F783CE4.1050908@fu-berlin.de> References:

<4F783CE4.1050908@fu-berlin.de> Date: Mon, 2 Apr 2012 14:34:00 -0400 Message-ID: From: ngs geek To: SeqAn Development Content-Type: multipart/alternative; boundary=e89a8ff1c37e15220f04bcb66f0f X-Originating-IP: 209.85.160.54 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1333391643-000018DE-99E444C8/0-0/0-0 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=0.5 required=5.0 tests=DNS_FROM_RFC_ABUSE, HTML_40_50, HTML_MESSAGE,RCVD_BY_IP,SPF_HELO_PASS,SPF_PASS Subject: Re: [Seqan-dev] Reading FastQ files from GZ archive 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, 02 Apr 2012 18:34:06 -0000 --e89a8ff1c37e15220f04bcb66f0f Content-Type: text/plain; charset=ISO-8859-1 Thanks for your help. I'm importing a pretty large number of fastq sequences in a fragmentstore, but again when I look at the PHRED score with getQualityValue(fragmentStore.readSeqStore[read_id][i]) I got inconsistent results. It looks like it assign different offset to each character: I'm working with illumina ( phred+64). Cheers JD On Sun, Apr 1, 2012 at 7:32 AM, Manuel Holtgrewe < manuel.holtgrewe@fu-berlin.de> wrote: > Dear JD, > > the DnaQ and Dna5Q alphabets are using PHRED scaled qualities. > > You should be able to read arbitrary qualities by giving an additional > CharString for the qualities to the readRecord function call: > > // ... > > > RecordReader, SinglePass<> > reader(fastq_file); > CharString id; > String seq; > CharString qual; > > if (readRecord(id, seq, qual, reader, Fastq()) != 0) > return 1; > > You then have to conver the qualities into PHRED scale manually and assign > them to the Dna5Q String seq. > > Another solution would be to convert the FASTQ files to PHRED scale in a > preprocessing step. > > There currently is not such functionality in SeqAn, but we plan to add > this in a later release. The main problem to tackle is how to perform a > robust guess about the quality scale -- it is not obvious which scale a > FASTQ file is in. > > HTH > Manuel > > > On 03/31/2012 10:35 PM, ngs geek wrote: > >> I forgot to add an example: >> >> raw quality string: >> bbbeeeeegfggfiiiiiiidgfagdghfd**fhdcdfdfb_ca`BOWU^GBBOLGLU_H_** >> Z_BLLLGLLFX]aNWWWY_bb_``**BBBBBBBBBBBBBBBBB >> >> seqan quality string: >> ______________________________**_____________!OWU^G!!OLGLU_H_** >> Z_!LLLGLLFX]_NWWWY______B!**BBBBBBBBBBBBBBB >> >> Best >> JD >> >> On Sat, Mar 31, 2012 at 3:39 PM, ngs geek > > wrote: >> >> Thanks! I'm seeing that the quality string is not the same that I >> read from the fastq file. >> Are they scaled? I read the doc here >> http://trac.seqan.de/wiki/**WhitePapers/QualityHandling >> but I can't figure out if these are guess by assignQualityValues ... >> in any case, I can't see >> consistent results for my Illumina 1.3+ reads. >> >> Thanks >> JD >> >> On Sat, Mar 31, 2012 at 5:22 AM, Holtgrewe, Manuel >> > >> >> wrote: >> >> Hi JD, >> >> good catch, you found a bug I just fixed. The problem was that >> assignQualityValues() did not resize the target string, it does >> now. Update your SVN checkout and it should work. >> >> Also, there now is a demo for reading FASTQ from gzipped files >> in core/demos/stream_read_fastq_**gz.cpp >> >> HTH >> Manuel >> >> ------------------------------**------------------------------** >> ------------ >> *From:* ngs geek [ngsgeek@gmail.com ] >> *Sent:* Friday, March 30, 2012 7:44 PM >> *To:* seqan-dev@lists.fu-berlin.de >> >> > >> *Subject:* [Seqan-dev] Reading FastQ files from GZ archive >> >> >> Hi All: >> >> I'm trying to filter reads contained in a gz file based on >> quality score; I was able to stream the id and the >> sequence with GZFile stream and using a singlepass reader (I >> don't want to keep the reads in memory). >> Unfortunately, I can't access the quality string. >> >> RecordReader, SinglePass<> > reader(fastq_file); >> CharString id; >> String seq; >> CharString qual; >> >> while (!atEnd(reader)) >> { >> if (readRecord(id, seq, reader, Fastq()) != 0) >> { >> std::cerr << "Problem with your FASTQ file." << std::endl; >> return 1; >> } >> >> // reading qual >> } >> >> Any idea on this? I tried assignQualities etc. with no luck. >> >> Thanks >> JD >> >> >> ______________________________**_________________ >> seqan-dev mailing list >> seqan-dev@lists.fu-berlin.de > 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 > --e89a8ff1c37e15220f04bcb66f0f Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Thanks for your help. I'm importing a pretty large number of fastq sequ= ences in a fragmentstore, but again when I look at the PHRED score with get= QualityValue(fragmentStore.readSeqStore[read_id][i])

I got inconsistent= results. It looks like it assign different offset to each character: I'= ;m working with illumina ( phred+64).

Cheers

On Sun, Apr 1, 2012 at 7:32 AM, Manuel Holtgrewe <= span dir=3D"ltr"><manue= l.holtgrewe@fu-berlin.de> wrote:

Dear JD,

the DnaQ and Dna5Q alphabets are using PHRED scaled qualities.

You should be able to read arbitrary qualities by giving an additional Char= String for the qualities to the readRecord function call:

// ...

RecordReader<Stream<GZFile>, SinglePass<> > reader(fastq_= file);
CharString id;
String<Dna5Q> seq;
CharString qual;

if (readRecord(id, seq, qual, reader, Fastq()) !=3D 0)
=A0 =A0return 1;

You then have to conver the qualities into PHRED scale manually and assign = them to the Dna5Q String seq.

Another solution would be to convert the FASTQ files to PHRED scale in a pr= eprocessing step.

There currently is not such functionality in SeqAn, but we plan to add this= in a later release. The main problem to tackle is how to perform a robust = guess about the quality scale -- it is not obvious which scale a FASTQ file= is in.

HTH
Manuel

On 03/31/2012 10:35 PM, ngs geek wrote:

I forgot to add an example:

raw quality string:
bbbeeeeegfggfiiiiiiidgfagdghfdfhdcdfdfb_ca`BOWU^GBBOLGLU_H_Z_= BLLLGLLFX]aNWWWY_bb_``BBBBBBBBBBBBBBBBB

seqan quality string:
___________________________________________!OWU^G!!OLGLU_H_Z_= !LLLGLLFX]_NWWWY______B!BBBBBBBBBBBBBBB

Best
JD

On Sat, Mar 31, 2012 at 3:39 PM, ngs geek <ngsgeek@gmail.com
<mailto:ngsgeek@g= mail.com>> wrote:

=A0 =A0Thanks! I'm seeing that the quality string is not the same that= I
=A0 =A0read from the fastq file.
=A0 =A0Are they scaled? I read the doc here
=A0 =A0http://trac.seqan.de/wiki/WhitePapers/QualityHandli= ng
=A0 =A0but I can't figure out if these are guess by assignQualityValue= s ...
=A0 =A0in any case, I can't see
=A0 =A0consistent results for my Illumina 1.3+ reads.

=A0 =A0Thanks
=A0 =A0JD

=A0 =A0On Sat, Mar 31, 2012 at 5:22 AM, Holtgrewe, Manuel
=A0 =A0<manuel.holtgrewe@fu-berlin.de
=A0 =A0<mailto:manuel.holtgrewe@fu-berlin.de>> wrote:

=A0 =A0 =A0 =A0Hi JD,

=A0 =A0 =A0 =A0good catch, you found a bug I just fixed. The problem was t= hat
=A0 =A0 =A0 =A0assignQualityValues() did not resize the target string, it = does
=A0 =A0 =A0 =A0now. Update your SVN checkout and it should work.

=A0 =A0 =A0 =A0Also, there now is a demo for reading FASTQ from gzipped fi= les
=A0 =A0 =A0 =A0in core/demos/stream_read_fastq_gz.cpp

=A0 =A0 =A0 =A0HTH
=A0 =A0 =A0 =A0Manuel

=A0 =A0 =A0 =A0----------------------------------------------------= --------------------
=A0 =A0 =A0 =A0*From:* ngs geek [ngsgeek@gmail.com <mailto:ngsgeek@gmail.com>]
=A0 =A0 =A0 =A0*Sent:* Friday, March 30, 2012 7:44 PM
=A0 =A0 =A0 =A0*To:* seqan-dev@lists.fu-berlin.de
=A0 =A0 =A0 =A0<mailto:seqan-dev@lists.fu-berlin.de>
=A0 =A0 =A0 =A0*Subject:* [Seqan-dev] Reading FastQ files from GZ archive<= div class=3D"im">

=A0 =A0 =A0 =A0Hi All:

=A0 =A0 =A0 =A0I'm trying to filter reads contained in a gz file based= on
=A0 =A0 =A0 =A0quality score; I was able to stream the id and the
=A0 =A0 =A0 =A0sequence with GZFile stream and using a singlepass reader (= I
=A0 =A0 =A0 =A0don't want to keep the reads in memory).
=A0 =A0 =A0 =A0Unfortunately, I can't access the quality string.

=A0 =A0 =A0 =A0RecordReader<Stream<GZFile>, SinglePass<> &g= t; reader(fastq_file);
=A0 =A0 =A0 =A0CharString id;
=A0 =A0 =A0 =A0String<Dna5Q> seq;
=A0 =A0 =A0 =A0CharString qual;

=A0 =A0 =A0 =A0while (!atEnd(reader))
=A0 =A0 =A0 =A0{
=A0 =A0 =A0 =A0if (readRecord(id, seq, reader, Fastq()) !=3D 0)
=A0 =A0 =A0 =A0{
=A0 =A0 =A0 =A0std::cerr << "Problem with your FASTQ file."= ; << std::endl;
=A0 =A0 =A0 =A0return 1;
=A0 =A0 =A0 =A0}

=A0 =A0 =A0 =A0// reading qual
=A0 =A0 =A0 =A0}

=A0 =A0 =A0 =A0Any idea on this? I tried assignQualities etc. with no luck= .

=A0 =A0 =A0 =A0Thanks
=A0 =A0 =A0 =A0JD

=A0 =A0 =A0 =A0_______________________________________________
=A0 =A0 =A0 =A0seqan-dev mailing list

=A0 =A0 =A0 =A0seqan-dev@lists.fu-berlin.de <mailto:seqan-dev@lists.fu-berlin.= de>
=A0 =A0 =A0 =A0https://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

--e89a8ff1c37e15220f04bcb66f0f-- From weese@campus.fu-berlin.de Tue Apr 10 11:05:12 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 <1SHX0g-0007kh-Cw>; Tue, 10 Apr 2012 11:05:10 +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 <1SHX0g-0000ac-8x>; Tue, 10 Apr 2012 11:05:10 +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 <1SHX0g-0005Bo-3F>; Tue, 10 Apr 2012 11:05:10 +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 14.02.0283.003; Tue, 10 Apr 2012 11:04:37 +0200 From: "Weese, David" To: SeqAn Development Thread-Topic: [Seqan-dev] ModifiedString question Thread-Index: AQHNEOOqdMdS44TqKEuGJ5qSk+lnoZaTrqQA Date: Tue, 10 Apr 2012 09:04:36 +0000 Message-ID: References: <4F799DEA.1010705@pasteur.fr> In-Reply-To: <4F799DEA.1010705@pasteur.fr> Accept-Language: de-DE, en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: text/plain; charset="iso-8859-1" Content-ID: <51F9CF17EB97A54E805A87A3E5892331@campus.fu-berlin.de> Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Originating-IP: 130.133.170.202 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1334048710-000018DE-AA266C6C/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Burundi.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: Re: [Seqan-dev] ModifiedString 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: Tue, 10 Apr 2012 09:05:12 -0000 Hi, yes, ModifiedStrings are a different type of sequences that are views to St= rings but aren't Strings itself and don't consume additional memory. You ne= ed to use a temporary "Dna5String tmp =3D revSeq1;" which you can pass. Alt= ernatively you could change the interface of your function to accept any se= quence, not only Dna5Strings. Cheers, David -- David Weese weese@inf.fu-berlin.de Freie Universit=E4t Berlin http://www.inf.fu-berlin.de/ Institut f=FCr Informatik Phone: +49 30 838 75246 Takustra=DFe 9 Algorithmic Bioinformatics 14195 Berlin Room 021=20 Am 02.04.2012 um 14:39 schrieb Bernd Jagla: > Hi, >=20 > I have the following function: >=20 > bool qualityThreshold(Dna5String& seq1, CharString& qual1, Dna5String& se= q2, CharString& qual2, > int qualityThreshold, int minLen, bool& pairedEnd, > int& countPrimeTrimmed, int& lengthConstrain ) { >=20 > now, I want to use the reverse sequence as an input using : >=20 > Dna5StringReverse revSeq1(seq1); >=20 > I guess I misunderstand something here, but it seems that Dna5StringRever= se is not returning a DNA5String but its own type... How can I convert the = Reverse in a regular DNA5String? >=20 > Thanks for the clarification, >=20 > Bernd >=20 >=20 >=20 > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev From bernd.jagla@pasteur.fr Tue Apr 10 13:58:19 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 <1SHZiE-0005FI-9C>; Tue, 10 Apr 2012 13:58:18 +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 <1SHZiE-0004J2-4y>; Tue, 10 Apr 2012 13:58:18 +0200 Received: from maroilles.sis.pasteur.fr (localhost [127.0.0.1]) by mail-interne3.pasteur.fr (Postfix) with ESMTP id 592B638104F for ; Tue, 10 Apr 2012 13:58:16 +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 34E4B381044 for ; Tue, 10 Apr 2012 13:58:16 +0200 (CEST) Message-ID: <4F842057.9080704@pasteur.fr> Date: Tue, 10 Apr 2012 13:58:15 +0200 From: Bernd Jagla User-Agent: Mozilla/5.0 (Windows NT 5.1; rv:11.0) Gecko/20120327 Thunderbird/11.0.1 MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de Content-Type: multipart/alternative; boundary="------------080203030509030802020306" X-Originating-IP: 157.99.64.82 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1334059098-000018DE-3ADD1993/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.184524, 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 X-Spam-Status: No, score=1.4 required=5.0 tests=DNS_FROM_RFC_POST, HTML_MESSAGE Subject: [Seqan-dev] resetting a stream 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, 10 Apr 2012 11:58:19 -0000 This is a multi-part message in MIME format. --------------080203030509030802020306 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Hi, Is it correct to reset a stream (bam file) using the following command: TStreamOrReader & reader streamSeek(reader, 0, SEEK_SET); Thanks for clarifying... I would like to reset a reader (TStreamOrReader, from bam_stats.cpp) and re-read a bam/sam file... Thanks, Bernd --------------080203030509030802020306 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi,

Is it correct to reset a stream (bam file) using the following command:

TStreamOrReader & reader streamSeek(reader, 0, SEEK_SET);Thanks for clarifying...

I would like to reset a reader (TStreamOrReader, from bam_stats.cpp) and re-read a bam/sam file...

Thanks,

Bernd
--------------080203030509030802020306-- From bernd.jagla@pasteur.fr Tue Apr 10 15:01:34 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 <1SHahR-0007XO-Bs>; Tue, 10 Apr 2012 15:01:33 +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 <1SHahR-0004E2-29>; Tue, 10 Apr 2012 15:01:33 +0200 Received: from maroilles.sis.pasteur.fr (localhost [127.0.0.1]) by mail-interne3.pasteur.fr (Postfix) with ESMTP id 83D7438104F for ; Tue, 10 Apr 2012 15:01:31 +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 3EAF3381044 for ; Tue, 10 Apr 2012 15:01:31 +0200 (CEST) Message-ID: <4F842F2B.6040105@pasteur.fr> Date: Tue, 10 Apr 2012 15:01:31 +0200 From: Bernd Jagla User-Agent: Mozilla/5.0 (Windows NT 5.1; rv:11.0) Gecko/20120327 Thunderbird/11.0.1 MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de Content-Type: multipart/mixed; boundary="------------070308060504080803010104" X-Originating-IP: 157.99.64.82 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1334062893-000018DE-995F4F3C/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.289266, 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 X-Spam-Status: No, score=1.4 required=5.0 tests=DNS_FROM_RFC_POST Subject: [Seqan-dev] sorting sam file by SortReadID() 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, 10 Apr 2012 13:01:34 -0000 This is a multi-part message in MIME format. --------------070308060504080803010104 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Hi, I am trying to sort a sam/bam file by read-id and am using the following construct: sortAlignedReads(reader, SortReadId()); Unfortunately the compiler is complaining: In file included from /pasteur/solexa2/solexa_travail/PF2/programs/seqan/workspace/seqan/core/include/seqan/store.h:63: /pasteur/solexa2/solexa_travail/PF2/programs/seqan/workspace/seqan/core/include/seqan/store/store_align.h:369:13: error: member reference base type 'const char' is not a structure or union return a1.readId < a2.readId; ~~ ^ /usr/lib/gcc/x86_64-redhat-linux6E/4.4.4/../../../../include/c++/4.4.4/bits/stl_algo.h:2128:8: note: in instantiation of member function 'seqan::_LessAlignedRead >::operator()' requested here if (__comp(__val, *__first)) ^ /usr/lib/gcc/x86_64-redhat-linux6E/4.4.4/../../../../include/c++/4.4.4/bits/stl_algo.h:3433:4: note: in instantiation of function template specialization 'std::__insertion_sort > >' requested here std::__insertion_sort(__first, __last, __comp); ^ /usr/lib/gcc/x86_64-redhat-linux6E/4.4.4/../../../../include/c++/4.4.4/bits/stl_algo.h:5468:2: note: in instantiation of function template specialization 'std::__inplace_stable_sort > >' requested here std::__inplace_stable_sort(__first, __last, __comp); ^ /pasteur/solexa2/solexa_travail/PF2/programs/seqan/workspace/seqan/core/include/seqan/store/store_align.h:433:2: note: in instantiation of function template specialization 'std::stable_sort > >' requested here std::stable_sort( ^ /pasteur/solexa2/solexa_travail/PF2/programs/seqan/workspace/seqan/sandbox/jagla/apps/sambamstat/sambamstat.h:286:5: note: in instantiation of function template specialization 'seqan::sortAlignedReads, seqan::SortReadId_>' requested here sortAlignedReads(reader, SortReadId()); ^ /pasteur/solexa2/solexa_travail/PF2/programs/seqan/workspace/seqan/sandbox/jagla/apps/sambamstat/sambamstat.h:340:16: note: in instantiation of function template specialization 'doWork, seqan::String, seqan::Alloc >, seqan::Owner >, seqan::Tag >' requested here return doWork(bamStream, seqs, options, Bam()); ^ 4 warnings and 15 errors generated. make[2]: *** [sandbox/jagla/apps/sambamstat/CMakeFiles/sambamstat.dir/sambamstat.cpp.o] Error 1 make[1]: *** [sandbox/jagla/apps/sambamstat/CMakeFiles/sambamstat.dir/all] Error 2 make: *** [all] Error 2 I also attach the the cpp and .h files.. Thanks for having a look at this ... Bernd --------------070308060504080803010104 Content-Type: text/plain; charset=windows-1252; name="sambamstat.h" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="sambamstat.h" // ========================================================================== // sambamstat // ========================================================================== // Copyright (c) 2006-2012, Knut Reinert, FU Berlin // All rights reserved. // // Redistribution and use in source and binary forms, with or without // modification, are permitted provided that the following conditions are met: // // * Redistributions of source code must retain the above copyright // notice, this list of conditions and the following disclaimer. // * Redistributions in binary form must reproduce the above copyright // notice, this list of conditions and the following disclaimer in the // documentation and/or other materials provided with the distribution. // * Neither the name of Knut Reinert or the FU Berlin nor the names of // its contributors may be used to endorse or promote products derived // from this software without specific prior written permission. // // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE // ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE // FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL // DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR // SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER // CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT // LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY // OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH // DAMAGE. // // ========================================================================== // Author: Your Name // ========================================================================== #ifndef SANDBOX_JAGLA_APPS_SAMBAMSTAT_SAMBAMSTAT_H_ #define SANDBOX_JAGLA_APPS_SAMBAMSTAT_SAMBAMSTAT_H_ #include #include #include #include #include // For printing SeqAn Strings. #include using namespace seqan; // ============================================================================ // Forwards // ============================================================================ // ============================================================================ // Tags, Classes, Enums // ============================================================================ enum Format { FORMAT_AUTO, FORMAT_SAM, FORMAT_BAM }; enum SortOrder { SORTORDER_NA, SORTORDER_ID, SORTORDER_POS }; struct Options { bool showHelp; bool showVersion; unsigned int verbosity; CharString inFileName; CharString outFileName; bool statistics; Format inFormat; SortOrder sortOrder; Options() { // Set defaults. showHelp = false; showVersion = false; verbosity = 0; statistics = false; inFileName = ""; outFileName = ""; statistics = false; inFormat = FORMAT_AUTO; sortOrder = SORTORDER_NA; } }; // ============================================================================ // Metafunctions // ============================================================================ // ============================================================================ // Functions // ============================================================================ void setupCommandLineParser(CommandLineParser & parser, Options const & options) { addVersionLine(parser, "0.1"); addTitleLine(parser, "**********************"); addTitleLine(parser, "* sambamstat *"); addTitleLine(parser, "**********************"); addTitleLine(parser, ""); addTitleLine(parser, "(c) 2012 by Bernd Jagla "); addUsageLine(parser, "[OPTIONS] -if inputFile -of outputFile"); addSection(parser, "Main Options"); addOption(parser, CommandLineOption("if", "input-file", "Input file.", OptionType::String | OptionType::Label, options.inFileName)); addOption(parser, CommandLineOption("S", "input-sam", "Input file is SAM (default: auto).", OptionType::Bool, options.inFormat == FORMAT_SAM)); addOption(parser, CommandLineOption("B", "input-bam", "Input file is BAM (default: auto).", OptionType::Bool, options.inFormat == FORMAT_BAM)); addOption(parser, CommandLineOption("sP", "sortOrderPos", "assume sorted by position", OptionType::Bool, options.sortOrder == SORTORDER_POS)); addOption(parser, CommandLineOption("sI", "sortOrderID", "assume sorted by ID", OptionType::Bool, options.sortOrder == SORTORDER_ID)); addOption(parser, CommandLineOption("of", "output-file", "Output file.", OptionType::String | OptionType::Label, options.outFileName)); addSection(parser, "optional parameters:"); addOption(parser, CommandLineOption("s", "stats", "Perform stats", OptionType::Bool, options.statistics)); addSection(parser, "General Options"); addOption(parser, CommandLineOption("vv", "very-verbose", "Very verbose output.", OptionType::Bool)); addOption(parser, CommandLineOption("v", "verbose", "verbose output.", OptionType::Bool)); requiredArguments(parser, 0); } int parseCommandLineAndCheck(Options & options, CommandLineParser & parser, int argc, char const ** argv) { bool stop = !parse(parser, argc, argv); if (stop) return 1; if (isSetLong(parser, "help")) { options.showHelp = true; return 0; } if (isSetLong(parser, "version")) { options.showVersion = true; return 0; } getOptionValueLong(parser, "input-file", options.inFileName); getOptionValueLong(parser, "output-file", options.outFileName); if (isSetLong(parser, "verbose")) options.verbosity = 1; if (isSetLong(parser, "very-verbose")) options.verbosity = 2; if (isSetLong(parser, "stats")) options.statistics = true; return 0; } struct Stats { __uint64 numRecords; __uint64 alignedRecords; String editDistanceHisto; String mismatchHisto; String insertHisto; String deletionHisto; String avrgQuality; Stats() : numRecords(0), alignedRecords(0) {} }; /* * Analyze read that are sorted by ID */ template int analyze_idSorted(TStreamOrReader & reader, StringSet & seqs, Options const & options, TFormat const & tag) { StringSet refNames; NameStoreCache > refNamesCache(refNames); BamIOContext > context(refNames, refNamesCache); String<__uint64> qualSum; // Read alignments. BamAlignmentRecord record; if (options.verbosity >= 2) std::cerr << "Reading alignments" << std::endl; Align align; __int64 reads = 0; // while (!atEnd(reader)) { // Read alignment record. if (readRecord(record, context, reader, tag) != 0) { std::cerr << "Could not read alignment!" << std::endl; return 1; } if (options.verbosity >= 2) write2(std::cerr, record, context, Sam()); } return 0; } /* * Analyze reads that are sorted by position */ template int analyze_posSorted(TStreamOrReader & reader, StringSet & seqs, Options const & options, TFormat const & tag) { StringSet refNames; NameStoreCache > refNamesCache(refNames); BamIOContext > context(refNames, refNamesCache); String<__uint64> qualSum; // Read alignments. BamAlignmentRecord record; if (options.verbosity >= 2) std::cerr << "Reading alignments" << std::endl; Align align; __int64 reads = 0; // while (!atEnd(reader)) { // Read alignment record. if (readRecord(record, context, reader, tag) != 0) { std::cerr << "Could not read alignment!" << std::endl; return 1; } if (options.verbosity >= 2) write2(std::cerr, record, context, Sam()); } return 0; } /* * Here we deal with the sorting and organizing different order of events... */ template int doWork(TStreamOrReader & reader, StringSet & seqs, Options const & options, TFormat const & tag) { StringSet refNames; NameStoreCache > refNamesCache(refNames); BamIOContext > context(refNames, refNamesCache); String<__uint64> qualSum; // Read header. BamHeader header; if (options.verbosity >= 2) std::cerr << "Reading header" << std::endl; if (readRecord(header, context, reader, tag) != 0) { std::cerr << "Could not read header!" << std::endl; return 1; } Stats stats; switch (options.sortOrder){ case SORTORDER_ID : analyze_idSorted(reader, seqs, options, tag); //TODO sort sortAlignedReads(reader, SortBeginPos()); analyze_posSorted(reader, seqs, options, tag); break; case SORTORDER_POS : analyze_posSorted(reader, seqs, options, tag); //TODO sort sortAlignedReads(reader, SortReadId()); analyze_idSorted(reader, seqs, options, tag); break; case SORTORDER_NA : //TODO sort sortAlignedReads(reader, SortReadId()); analyze_idSorted(reader, seqs, options, tag); //TODO sort sortAlignedReads(reader, SortBeginPos()); analyze_posSorted(reader, seqs, options, tag); break; } return 0; } int mainWithOptions(Options & options) { typedef Iterator >::Type TIterator; std::cout << "Non-option Arguments:" << std::endl; std::cout << " input file: \"" << options.inFileName << "\"" << std::endl; std::cout << " output file: \"" << options.outFileName << "\"" << std::endl; std::cout << "Option Arguments:" << std::endl; StringSet seqIds; StringSet seqs; String > seqMMapString; if (options.inFormat == FORMAT_SAM) { if (options.verbosity >= 2) std::cerr << "Opening SAM file " << options.inFileName << std::endl; String > samMMapString; if (!open(samMMapString, toCString(options.inFileName), OPEN_RDONLY)) { std::cerr << "Could not open " << options.inFileName << std::endl; return 1; } RecordReader >, SinglePass > samReader(samMMapString); return doWork(samReader, seqs, options, Sam()); } else // options.inFormat == FORMAT_BAM { if (options.verbosity >= 2) std::cerr << "Opening BAM file " << options.inFileName << std::endl; Stream bamStream; if (!open(bamStream, toCString(options.inFileName), "r")) { std::cerr << "Could not open " << options.inFileName << std::endl; return 1; } return doWork(bamStream, seqs, options, Bam()); } return 0; } #endif // #ifndef SANDBOX_JAGLA_APPS_SAMBAMSTAT_SAMBAMSTAT_H_ --------------070308060504080803010104 Content-Type: text/plain; charset=windows-1252; name="sambamstat.cpp" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="sambamstat.cpp" // ========================================================================== // sambamstat // ========================================================================== // Copyright (c) 2006-2012, Knut Reinert, FU Berlin // All rights reserved. // // Redistribution and use in source and binary forms, with or without // modification, are permitted provided that the following conditions are met: // // * Redistributions of source code must retain the above copyright // notice, this list of conditions and the following disclaimer. // * Redistributions in binary form must reproduce the above copyright // notice, this list of conditions and the following disclaimer in the // documentation and/or other materials provided with the distribution. // * Neither the name of Knut Reinert or the FU Berlin nor the names of // its contributors may be used to endorse or promote products derived // from this software without specific prior written permission. // // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE // ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE // FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL // DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR // SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER // CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT // LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY // OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH // DAMAGE. // // ========================================================================== // Author: Your Name // ========================================================================== #include #include #include #include "sambamstat.h" using namespace seqan; // Program entry point int main(int argc, char const ** argv) { // Setup command line parser. CommandLineParser parser; Options options; setupCommandLineParser(parser, options); // Then, parse the command line and handle the cases where help display // is requested or erroneous parameters were given. int ret = parseCommandLineAndCheck(options, parser, argc, argv); if (ret != 0) { std::cerr << "Invalid usage!" << std::endl; return ret; } if (options.showHelp || options.showVersion) return 0; if (options.inFormat == FORMAT_AUTO) { std::ifstream guessIn(toCString(options.inFileName), std::ios::binary | std::ios::in); if (!guessIn.good()) { std::cerr << "Could not open " << options.inFileName << std::endl; return 1; } CharString magic; resize(magic, 2); guessIn.read(&magic[0], 2); if (magic != "\x1f\x8b") // Is not gzip-compressed. options.inFormat = FORMAT_SAM; else options.inFormat = FORMAT_BAM; } // Finally, launch the program. ret = mainWithOptions(options); return ret; } --------------070308060504080803010104-- From manuel.holtgrewe@fu-berlin.de Tue Apr 10 16:40:51 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 <1SHcFW-0002KT-Vl>; Tue, 10 Apr 2012 16:40:51 +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 <1SHcFW-0007dw-Sn>; Tue, 10 Apr 2012 16:40:50 +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 <1SHcFW-0004xl-Fe>; Tue, 10 Apr 2012 16:40:50 +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 14.02.0283.003; Tue, 10 Apr 2012 16:40:49 +0200 From: "Holtgrewe, Manuel" To: SeqAn Development Thread-Topic: [Seqan-dev] sorting sam file by SortReadID() Thread-Index: AQHNFxoa3SUXVKrV6k+T3k+EToyPPJaUIWxT Date: Tue, 10 Apr 2012 14:40:49 +0000 Message-ID: References: <4F842F2B.6040105@pasteur.fr> In-Reply-To: <4F842F2B.6040105@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::1334068850-000018DE-F5D58D36/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.228488, 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] sorting sam file by SortReadID() 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, 10 Apr 2012 14:40:51 -0000 This is meant for sorting alignments in the FragmentStore.=0A= =0A= You currently have to resort to an external tool for sorting SAM files with= out completely loading them into memory.=0A= =0A= *m=0A= ________________________________________=0A= From: Bernd Jagla [bernd.jagla@pasteur.fr]=0A= Sent: Tuesday, April 10, 2012 3:01 PM=0A= To: seqan-dev@lists.fu-berlin.de=0A= Subject: [Seqan-dev] sorting sam file by SortReadID()=0A= =0A= Hi,=0A= =0A= I am trying to sort a sam/bam file by read-id and am using the following=0A= construct:=0A= =0A= sortAlignedReads(reader, SortReadId());=0A= =0A= =0A= =0A= Unfortunately the compiler is complaining:=0A= =0A= In file included from=0A= /pasteur/solexa2/solexa_travail/PF2/programs/seqan/workspace/seqan/core/inc= lude/seqan/store.h:63:=0A= /pasteur/solexa2/solexa_travail/PF2/programs/seqan/workspace/seqan/core/inc= lude/seqan/store/store_align.h:369:13:=0A= error: member reference base type 'const char' is not a=0A= structure or union=0A= return a1.readId < a2.readId;=0A= ~~ ^=0A= /usr/lib/gcc/x86_64-redhat-linux6E/4.4.4/../../../../include/c++/4.4.4/bits= /stl_algo.h:2128:8:=0A= note: in instantiation of member function 'seqan::_LessAlignedRead >::operator()' requested here= =0A= if (__comp(__val, *__first))=0A= ^=0A= /usr/lib/gcc/x86_64-redhat-linux6E/4.4.4/../../../../include/c++/4.4.4/bits= /stl_algo.h:3433:4:=0A= note: in instantiation of function template specialization=0A= 'std::__insertion_sort > >' requested here=0A= std::__insertion_sort(__first, __last, __comp);=0A= ^=0A= /usr/lib/gcc/x86_64-redhat-linux6E/4.4.4/../../../../include/c++/4.4.4/bits= /stl_algo.h:5468:2:=0A= note: in instantiation of function template specialization=0A= 'std::__inplace_stable_sort > >' requested here=0A= std::__inplace_stable_sort(__first, __last, __comp);=0A= ^=0A= /pasteur/solexa2/solexa_travail/PF2/programs/seqan/workspace/seqan/core/inc= lude/seqan/store/store_align.h:433:2:=0A= note: in instantiation of function template=0A= specialization 'std::stable_sort > >'=0A= requested here=0A= std::stable_sort(=0A= ^=0A= /pasteur/solexa2/solexa_travail/PF2/programs/seqan/workspace/seqan/sandbox/= jagla/apps/sambamstat/sambamstat.h:286:5:=0A= note: in instantiation of function template=0A= specialization 'seqan::sortAlignedReads,=0A= seqan::SortReadId_>' requested here=0A= sortAlignedReads(reader, SortReadId());=0A= ^=0A= /pasteur/solexa2/solexa_travail/PF2/programs/seqan/workspace/seqan/sandbox/= jagla/apps/sambamstat/sambamstat.h:340:16:=0A= note: in instantiation of function template=0A= specialization 'doWork,=0A= seqan::String,=0A= seqan::Alloc >,=0A= seqan::Owner >,=0A= seqan::Tag >' requested here=0A= return doWork(bamStream, seqs, options, Bam());=0A= ^=0A= 4 warnings and 15 errors generated.=0A= make[2]: ***=0A= [sandbox/jagla/apps/sambamstat/CMakeFiles/sambamstat.dir/sambamstat.cpp.o]= =0A= Error 1=0A= make[1]: ***=0A= [sandbox/jagla/apps/sambamstat/CMakeFiles/sambamstat.dir/all] Error 2=0A= make: *** [all] Error 2=0A= =0A= I also attach the the cpp and .h files..=0A= =0A= Thanks for having a look at this ...=0A= =0A= Bernd=0A= From manuel.holtgrewe@fu-berlin.de Tue Apr 10 16:41:56 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 <1SHcGa-0002N6-1J>; Tue, 10 Apr 2012 16:41:56 +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 <1SHcGZ-0007s4-SQ>; Tue, 10 Apr 2012 16:41:56 +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 <1SHcGZ-00052k-La>; Tue, 10 Apr 2012 16:41:55 +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 14.02.0283.003; Tue, 10 Apr 2012 16:41:54 +0200 From: "Holtgrewe, Manuel" To: SeqAn Development Thread-Topic: [Seqan-dev] resetting a stream Thread-Index: AQHNFxE+0Hrxj7j3S0yA1JuPJk2ampaUIfsz Date: Tue, 10 Apr 2012 14:41:53 +0000 Message-ID: References: <4F842057.9080704@pasteur.fr> In-Reply-To: <4F842057.9080704@pasteur.fr> Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: multipart/alternative; boundary="_000_FCCAB9D80C3DAB47B5601C5B0E62872B070130EX02Acampusfuberl_" 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::1334068916-000018DE-1236C700/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.021948, 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,HTML_MESSAGE Subject: Re: [Seqan-dev] resetting a stream 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, 10 Apr 2012 14:41:56 -0000 --_000_FCCAB9D80C3DAB47B5601C5B0E62872B070130EX02Acampusfuberl_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Yes, this should work. ________________________________ From: Bernd Jagla [bernd.jagla@pasteur.fr] Sent: Tuesday, April 10, 2012 1:58 PM To: seqan-dev@lists.fu-berlin.de Subject: [Seqan-dev] resetting a stream Hi, Is it correct to reset a stream (bam file) using the following command: TStreamOrReader & reader streamSeek(reader, 0, SEEK_SET); Thanks for clarifying... I would like to reset a reader (TStreamOrReader, from bam_stats.cpp) and re= -read a bam/sam file... Thanks, Bernd --_000_FCCAB9D80C3DAB47B5601C5B0E62872B070130EX02Acampusfuberl_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Yes, this should work.

From: Bernd Jagla [bernd.jagla@pasteur.f= r]
Sent: Tuesday, April 10, 2012 1:58 PM
To: seqan-dev@lists.fu-berlin.de
Subject: [Seqan-dev] resetting a stream

Hi,

Is it correct to reset a stream (bam file) using the following comman= d:

TStreamOrReader & reader st= reamSeek(reader, 0, SEEK_SET);Thanks for clarifying...

I would like to reset a reader (TStreamOrReader, from bam_stats.cpp) and re= -read a bam/sam file...

Thanks,

Bernd

--_000_FCCAB9D80C3DAB47B5601C5B0E62872B070130EX02Acampusfuberl_-- From bernd.jagla@pasteur.fr Tue Apr 10 17:04:46 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 <1SHccf-00039q-H6>; Tue, 10 Apr 2012 17:04:45 +0200 Received: from mail-interne2.pasteur.fr ([157.99.64.81]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1SHccf-0003vq-At>; Tue, 10 Apr 2012 17:04:45 +0200 Received: from langres.sis.pasteur.fr (localhost [127.0.0.1]) by mail-interne2.pasteur.fr (Postfix) with ESMTP id 1A573E04B4; Tue, 10 Apr 2012 17:04:43 +0200 (CEST) X-Virus-Scanned: amavisd-new at pasteur.fr Received: from [192.168.0.12] (vir78-2-82-247-223-88.fbx.proxad.net [82.247.223.88]) (using TLSv1 with cipher AES128-SHA (128/128 bits)) (No client certificate requested) by mail-interne2.pasteur.fr (Postfix) with ESMTPSA id B7053E049F; Tue, 10 Apr 2012 17:04:42 +0200 (CEST) Mime-Version: 1.0 (Apple Message framework v1257) Content-Type: text/plain; charset=us-ascii From: Bernd Jagla In-Reply-To: Date: Tue, 10 Apr 2012 17:04:42 +0200 Content-Transfer-Encoding: quoted-printable Message-Id: References: <4F842F2B.6040105@pasteur.fr> To: SeqAn Development X-Mailer: Apple Mail (2.1257) X-Originating-IP: 157.99.64.81 X-purgate: suspect X-purgate-type: suspect X-purgate-ID: 151147::1334070285-000018DE-B0C1DB16/3551123337-0/0-1 X-Bogosity: Ham, tests=bogofilter, spamicity=0.098550, 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: xx X-Spam-Status: No, score=2.4 required=5.0 tests=DNS_FROM_RFC_POST, FU_XPURGATE_SUSP Subject: Re: [Seqan-dev] sorting sam file by SortReadID() 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, 10 Apr 2012 15:04:46 -0000 With external do you mean something like samtools or sort, i.e. through = the command line? B On Apr 10, 2012, at 4:40 PM, Holtgrewe, Manuel wrote: > This is meant for sorting alignments in the FragmentStore. >=20 > You currently have to resort to an external tool for sorting SAM files = without completely loading them into memory. >=20 > *m > ________________________________________ > From: Bernd Jagla [bernd.jagla@pasteur.fr] > Sent: Tuesday, April 10, 2012 3:01 PM > To: seqan-dev@lists.fu-berlin.de > Subject: [Seqan-dev] sorting sam file by SortReadID() >=20 > Hi, >=20 > I am trying to sort a sam/bam file by read-id and am using the = following > construct: >=20 > sortAlignedReads(reader, SortReadId()); >=20 >=20 >=20 > Unfortunately the compiler is complaining: >=20 > In file included from > = /pasteur/solexa2/solexa_travail/PF2/programs/seqan/workspace/seqan/core/in= clude/seqan/store.h:63: > = /pasteur/solexa2/solexa_travail/PF2/programs/seqan/workspace/seqan/core/in= clude/seqan/store/store_align.h:369:13: > error: member reference base type 'const char' is not a > structure or union > return a1.readId < a2.readId; > ~~ ^ > = /usr/lib/gcc/x86_64-redhat-linux6E/4.4.4/../../../../include/c++/4.4.4/bit= s/stl_algo.h:2128:8: > note: in instantiation of member function = 'seqan::_LessAlignedRead const seqan::Tag >::operator()' requested = here > if (__comp(__val, *__first)) > ^ > = /usr/lib/gcc/x86_64-redhat-linux6E/4.4.4/../../../../include/c++/4.4.4/bit= s/stl_algo.h:3433:4: > note: in instantiation of function template specialization > 'std::__insertion_sort const seqan::Tag > >' requested here > std::__insertion_sort(__first, __last, __comp); > ^ > = /usr/lib/gcc/x86_64-redhat-linux6E/4.4.4/../../../../include/c++/4.4.4/bit= s/stl_algo.h:5468:2: > note: in instantiation of function template specialization > 'std::__inplace_stable_sort const seqan::Tag > >' requested here > std::__inplace_stable_sort(__first, __last, __comp); > ^ > = /pasteur/solexa2/solexa_travail/PF2/programs/seqan/workspace/seqan/core/in= clude/seqan/store/store_align.h:433:2: > note: in instantiation of function template > specialization 'std::stable_sort seqan::_LessAlignedRead > = >' > requested here > std::stable_sort( > ^ > = /pasteur/solexa2/solexa_travail/PF2/programs/seqan/workspace/seqan/sandbox= /jagla/apps/sambamstat/sambamstat.h:286:5: > note: in instantiation of function template > specialization 'seqan::sortAlignedReads, > seqan::SortReadId_>' requested here > sortAlignedReads(reader, SortReadId()); > ^ > = /pasteur/solexa2/solexa_travail/PF2/programs/seqan/workspace/seqan/sandbox= /jagla/apps/sambamstat/sambamstat.h:340:16: > note: in instantiation of function template > specialization 'doWork, > seqan::String, > seqan::Alloc >, > seqan::Owner >, > seqan::Tag >' requested here > return doWork(bamStream, seqs, options, Bam()); > ^ > 4 warnings and 15 errors generated. > make[2]: *** > = [sandbox/jagla/apps/sambamstat/CMakeFiles/sambamstat.dir/sambamstat.cpp.o]= > Error 1 > make[1]: *** > [sandbox/jagla/apps/sambamstat/CMakeFiles/sambamstat.dir/all] Error 2 > make: *** [all] Error 2 >=20 > I also attach the the cpp and .h files.. >=20 > Thanks for having a look at this ... >=20 > Bernd >=20 > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev From manuel.holtgrewe@fu-berlin.de Tue Apr 10 17:51:21 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 <1SHdLk-0004iU-ME>; Tue, 10 Apr 2012 17:51:20 +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 <1SHdLk-0005SS-JV>; Tue, 10 Apr 2012 17:51:20 +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 <1SHdLk-00024B-DM>; Tue, 10 Apr 2012 17:51:20 +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 14.02.0283.003; Tue, 10 Apr 2012 17:51:14 +0200 From: "Holtgrewe, Manuel" To: SeqAn Development Thread-Topic: [Seqan-dev] sorting sam file by SortReadID() Thread-Index: AQHNFxoa3SUXVKrV6k+T3k+EToyPPJaUIWxT///lXACAAC5xMw== Date: Tue, 10 Apr 2012 15:51:14 +0000 Message-ID: References: <4F842F2B.6040105@pasteur.fr> , 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: suspect X-purgate-type: suspect X-purgate-ID: 151147::1334073080-000018DE-BB3E0DAC/3551123337-0/0-1 X-Bogosity: Ham, tests=bogofilter, spamicity=0.159983, 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] sorting sam file by SortReadID() 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, 10 Apr 2012 15:51:21 -0000 Yes, or a non-SeqAn library.=0A= ________________________________________=0A= From: Bernd Jagla [bernd.jagla@pasteur.fr]=0A= Sent: Tuesday, April 10, 2012 5:04 PM=0A= To: SeqAn Development=0A= Subject: Re: [Seqan-dev] sorting sam file by SortReadID()=0A= =0A= With external do you mean something like samtools or sort, i.e. through the= command line?=0A= =0A= B=0A= On Apr 10, 2012, at 4:40 PM, Holtgrewe, Manuel wrote:=0A= =0A= > This is meant for sorting alignments in the FragmentStore.=0A= >=0A= > You currently have to resort to an external tool for sorting SAM files wi= thout completely loading them into memory.=0A= >=0A= > *m=0A= > ________________________________________=0A= > From: Bernd Jagla [bernd.jagla@pasteur.fr]=0A= > Sent: Tuesday, April 10, 2012 3:01 PM=0A= > To: seqan-dev@lists.fu-berlin.de=0A= > Subject: [Seqan-dev] sorting sam file by SortReadID()=0A= >=0A= > Hi,=0A= >=0A= > I am trying to sort a sam/bam file by read-id and am using the following= =0A= > construct:=0A= >=0A= > sortAlignedReads(reader, SortReadId());=0A= >=0A= >=0A= >=0A= > Unfortunately the compiler is complaining:=0A= >=0A= > In file included from=0A= > /pasteur/solexa2/solexa_travail/PF2/programs/seqan/workspace/seqan/core/i= nclude/seqan/store.h:63:=0A= > /pasteur/solexa2/solexa_travail/PF2/programs/seqan/workspace/seqan/core/i= nclude/seqan/store/store_align.h:369:13:=0A= > error: member reference base type 'const char' is not a=0A= > structure or union=0A= > return a1.readId < a2.readId;=0A= > ~~ ^=0A= > /usr/lib/gcc/x86_64-redhat-linux6E/4.4.4/../../../../include/c++/4.4.4/bi= ts/stl_algo.h:2128:8:=0A= > note: in instantiation of member function 'seqan::_LessAlignedRead const seqan::Tag >::operator()' requested here= =0A= > if (__comp(__val, *__first))=0A= > ^=0A= > /usr/lib/gcc/x86_64-redhat-linux6E/4.4.4/../../../../include/c++/4.4.4/bi= ts/stl_algo.h:3433:4:=0A= > note: in instantiation of function template specialization=0A= > 'std::__insertion_sort const seqan::Tag > >' requested here=0A= > std::__insertion_sort(__first, __last, __comp);=0A= > ^=0A= > /usr/lib/gcc/x86_64-redhat-linux6E/4.4.4/../../../../include/c++/4.4.4/bi= ts/stl_algo.h:5468:2:=0A= > note: in instantiation of function template specialization=0A= > 'std::__inplace_stable_sort const seqan::Tag > >' requested here=0A= > std::__inplace_stable_sort(__first, __last, __comp);=0A= > ^=0A= > /pasteur/solexa2/solexa_travail/PF2/programs/seqan/workspace/seqan/core/i= nclude/seqan/store/store_align.h:433:2:=0A= > note: in instantiation of function template=0A= > specialization 'std::stable_sort seqan::_LessAlignedRead > >'= =0A= > requested here=0A= > std::stable_sort(=0A= > ^=0A= > /pasteur/solexa2/solexa_travail/PF2/programs/seqan/workspace/seqan/sandbo= x/jagla/apps/sambamstat/sambamstat.h:286:5:=0A= > note: in instantiation of function template=0A= > specialization 'seqan::sortAlignedReads,=0A= > seqan::SortReadId_>' requested here=0A= > sortAlignedReads(reader, SortReadId());=0A= > ^=0A= > /pasteur/solexa2/solexa_travail/PF2/programs/seqan/workspace/seqan/sandbo= x/jagla/apps/sambamstat/sambamstat.h:340:16:=0A= > note: in instantiation of function template=0A= > specialization 'doWork,=0A= > seqan::String,=0A= > seqan::Alloc >,=0A= > seqan::Owner >,=0A= > seqan::Tag >' requested here=0A= > return doWork(bamStream, seqs, options, Bam());=0A= > ^=0A= > 4 warnings and 15 errors generated.=0A= > make[2]: ***=0A= > [sandbox/jagla/apps/sambamstat/CMakeFiles/sambamstat.dir/sambamstat.cpp.o= ]=0A= > Error 1=0A= > make[1]: ***=0A= > [sandbox/jagla/apps/sambamstat/CMakeFiles/sambamstat.dir/all] Error 2=0A= > make: *** [all] Error 2=0A= >=0A= > I also attach the the cpp and .h files..=0A= >=0A= > Thanks for having a look at this ...=0A= >=0A= > Bernd=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= _______________________________________________=0A= seqan-dev mailing list=0A= seqan-dev@lists.fu-berlin.de=0A= https://lists.fu-berlin.de/listinfo/seqan-dev=0A= From ananth.ccamp@gmail.com Fri Apr 13 12:22:02 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 <1SIddg-0006eR-Rt>; Fri, 13 Apr 2012 12:22:00 +0200 Received: from mail-wg0-f50.google.com ([74.125.82.50]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1SIddg-0004me-O1>; Fri, 13 Apr 2012 12:22:00 +0200 Received: by wgbds12 with SMTP id ds12so2862932wgb.31 for ; Fri, 13 Apr 2012 03:21:59 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:sender:date:x-google-sender-auth:message-id:subject :from:to:content-type; bh=dpXbN9pk8111ZVa7Fq6/gYXoHifvVwyfWyLfC8dxMWc=; b=Wdgh7gBmmmGRSalLC4LUZAOon5TAhUxP3mbtrU+8sREjGIQ6Cye/zetNY57bjkMraa EC3BgzNSOjQY7TJdiRLg7HdId/1WDXg/9kJUUCcjTDedzZSJJoHmVTqZnv7W19zmGAzc vfjZ0sBeweB9g2xBNVPZpegGUxDRdOT1PmEgxROvPaqsnIt9gxgSCoCYY/ttpcjS6vnR df4ZG72l1iQ86f/zlHTX6yGkRaxvK49EBBs9C3PrcSEUCIj8X5/vsrPU3ARKU76CuPRX 3AB1k56wI0H0oZASQWN0FFg+VCd8cTUIvN5oAsss41p+F0FZR9q7vdKTsDFUmV/rhnEm qqvA== MIME-Version: 1.0 Received: by 10.180.95.34 with SMTP id dh2mr2537892wib.15.1334312519464; Fri, 13 Apr 2012 03:21:59 -0700 (PDT) Sender: ananth.ccamp@gmail.com Received: by 10.180.6.200 with HTTP; Fri, 13 Apr 2012 03:21:59 -0700 (PDT) Date: Fri, 13 Apr 2012 15:51:59 +0530 X-Google-Sender-Auth: TPnzex7bnFeyRgp3zdAVgicgcrY Message-ID: From: Anantharamanan R To: seqan-dev@lists.fu-berlin.de Content-Type: multipart/alternative; boundary=f46d04448035bdf85104bd8cd7e1 X-Originating-IP: 74.125.82.50 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1334312520-000018DE-D46ACCB9/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.277251, 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=0.7 required=5.0 tests=DNS_FROM_RFC_ABUSE, HTML_10_20, HTML_MESSAGE,RCVD_BY_IP,SPF_HELO_PASS,SPF_PASS Subject: [Seqan-dev] SNP and Indel location 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, 13 Apr 2012 10:22:02 -0000 --f46d04448035bdf85104bd8cd7e1 Content-Type: text/plain; charset=ISO-8859-1 Dear All, I am simulating illumina reads with -hs, -hi (default rate 0.001). I want to know where exactly these variants are introduced (Location) into my genome during simulation. It would be really great if somebody help me to trace this. Regards Ananth --f46d04448035bdf85104bd8cd7e1 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear All,

=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 I am simulating il= lumina reads with=A0 -hs, -hi (default rate 0.001). I want to know where exactly these variants=20 are introduced (Location) into my genome during simulation. It would be rea= lly great if=20 somebody help me to trace this.

Regards
Ananth=20 --f46d04448035bdf85104bd8cd7e1-- From manuel.holtgrewe@fu-berlin.de Fri Apr 13 12:52:20 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 <1SIe71-0007hg-AM>; Fri, 13 Apr 2012 12:52:19 +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 <1SIe71-0003C2-5x>; Fri, 13 Apr 2012 12:52:19 +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 <1SIe70-0001Dr-VU>; Fri, 13 Apr 2012 12:52:19 +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 14.02.0283.003; Fri, 13 Apr 2012 12:52:17 +0200 From: "Holtgrewe, Manuel" To: SeqAn Development Thread-Topic: [Seqan-dev] SNP and Indel location Thread-Index: AQHNGV9L57nTaPOqnke+dg/lIkr3l5aYk93Y Date: Fri, 13 Apr 2012 10:52:17 +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: multipart/alternative; boundary="_000_FCCAB9D80C3DAB47B5601C5B0E62872B070D8BEX02Acampusfuberl_" MIME-Version: 1.0 X-Originating-IP: 130.133.170.203 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1334314339-000018DE-FC3CA01C/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000744, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Algerien.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=ALL_TRUSTED,HTML_50_60, HTML_MESSAGE Subject: Re: [Seqan-dev] SNP and Indel location 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, 13 Apr 2012 10:52:20 -0000 --_000_FCCAB9D80C3DAB47B5601C5B0E62872B070D8BEX02Acampusfuberl_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Ananth, This is currently not possible using mason. I would also recommend to use an external tool for simulating SNPs since ma= son does not do indels that keep the reading frame (i.e. most lengths shoul= d be multiples of 3) etc. For read mapping, this is sufficient, for SNP det= ection, it is most probably not. *m ________________________________ From: Anantharamanan R [ananthr@ncbs.res.in] Sent: Friday, April 13, 2012 12:21 PM To: seqan-dev@lists.fu-berlin.de Subject: [Seqan-dev] SNP and Indel location Dear All, I am simulating illumina reads with -hs, -hi (default rate 0= .001). I want to know where exactly these variants are introduced (Location= ) into my genome during simulation. It would be really great if somebody he= lp me to trace this. Regards Ananth --_000_FCCAB9D80C3DAB47B5601C5B0E62872B070D8BEX02Acampusfuberl_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Ananth,

This is currently not possible using mason.

I would also recommend to use an external tool for simulating SNPs sin= ce mason does not do indels that keep the reading frame (i.e. most lengths = should be multiples of 3) etc. For read mapping, this is sufficient, for SN= P detection, it is most probably not.

From: Anantharamanan R [ananthr@ncbs.res= .in]
Sent: Friday, April 13, 2012 12:21 PM
To: seqan-dev@lists.fu-berlin.de
Subject: [Seqan-dev] SNP and Indel location

Dear All,

&nb= sp; I am simulating illumina reads with -hs, -hi (default rate 0.001)= . I want to know where exactly these variants are introduced (Location) int= o my genome during simulation. It would be really great if somebody help me= to trace this.

Regards
Ananth

--_000_FCCAB9D80C3DAB47B5601C5B0E62872B070D8BEX02Acampusfuberl_-- From manuel.holtgrewe@fu-berlin.de Tue Apr 17 17:52:10 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 <1SKAhN-0005Ot-Al>; Tue, 17 Apr 2012 17:52:09 +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 <1SKAhN-0000Lq-82>; Tue, 17 Apr 2012 17:52:09 +0200 Received: from ecoli.imp.fu-berlin.de ([160.45.111.133]) by inpost2.zedat.fu-berlin.de (Exim 4.69) with esmtpsa (envelope-from ) id <1SKAhN-0004cv-5V>; Tue, 17 Apr 2012 17:52:09 +0200 Message-ID: <4F8D913C.9080305@fu-berlin.de> Date: Tue, 17 Apr 2012 17:50:20 +0200 From: Manuel Holtgrewe User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:11.0) Gecko/20120329 Thunderbird/11.0.1 MIME-Version: 1.0 To: SeqAn Development References:

<4F783CE4.1050908@fu-berlin.de> In-Reply-To: Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Originating-IP: 160.45.111.133 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1334677929-000018DE-3DEDBC47/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.010694, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Algerien.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: Re: [Seqan-dev] Reading FastQ files from GZ archive 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, 17 Apr 2012 15:52:10 -0000 JD, we only support PHRED scores at the moment. You have to convert your FASTQ reads to PHRED/SANGER qualities before importing them using fragment store. *m From bernd.jagla@pasteur.fr Wed Apr 18 14:32:00 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 <1SKU3D-0001tc-Hb>; Wed, 18 Apr 2012 14:31:59 +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 <1SKU3D-0007sS-Do>; Wed, 18 Apr 2012 14:31:59 +0200 Received: from maroilles.sis.pasteur.fr (localhost [127.0.0.1]) by mail-interne3.pasteur.fr (Postfix) with ESMTP id A684738105B for ; Wed, 18 Apr 2012 14:31:57 +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 6B92B381059 for ; Wed, 18 Apr 2012 14:31:57 +0200 (CEST) Message-ID: <4F8EB43F.6000702@pasteur.fr> Date: Wed, 18 Apr 2012 14:31:59 +0200 From: Bernd Jagla User-Agent: Mozilla/5.0 (Windows NT 5.1; rv:11.0) Gecko/20120327 Thunderbird/11.0.1 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::1334752319-000018DE-32ED0C1E/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.103487, 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 X-Spam-Status: No, score=1.4 required=5.0 tests=DNS_FROM_RFC_POST Subject: [Seqan-dev] compile problem 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, 18 Apr 2012 12:32:00 -0000 I am getting the following error after a svn checkout (now revision 11686) [ 45%] Building CXX object core/demos/CMakeFiles/sam2svg.dir/sam2svg.cpp.o In file included from /pasteur/solexa2/solexa_travail/PF2/programs/seqan/workspace/seqan/core/demos/sam2svg.cpp:8: /pasteur/solexa2/solexa_travail/PF2/programs/seqan/workspace/seqan/core/include/seqan/misc/misc_svg.h:124:13: error: no function template matches function template specialization 'svgResize' inline void svgResize(SVGFile &svg, int width, int height) ^ Could you please let me know when this is fixed? thanks, Bernd From manuel.holtgrewe@fu-berlin.de Wed Apr 18 14:54:41 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 <1SKUPA-0002io-4O>; Wed, 18 Apr 2012 14:54:40 +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 <1SKUPA-0006lY-0v>; Wed, 18 Apr 2012 14:54:40 +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 <1SKUP9-0004ce-Q6>; Wed, 18 Apr 2012 14:54:40 +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 14.02.0283.003; Wed, 18 Apr 2012 14:53:36 +0200 From: "Holtgrewe, Manuel" To: SeqAn Development Thread-Topic: [Seqan-dev] compile problem Thread-Index: AQHNHV9GXfqNeptCxk+kuxZLxe5YK5agiakw Date: Wed, 18 Apr 2012 12:53:35 +0000 Message-ID: References: <4F8EB43F.6000702@pasteur.fr> In-Reply-To: <4F8EB43F.6000702@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::1334753680-000018DE-536814F6/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.001412, 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] compile problem 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, 18 Apr 2012 12:54:41 -0000 Without a minimal example program and the whole compiler output we will not= be able to help you.=0A= ________________________________________=0A= From: Bernd Jagla [bernd.jagla@pasteur.fr]=0A= Sent: Wednesday, April 18, 2012 2:31 PM=0A= To: seqan-dev@lists.fu-berlin.de=0A= Subject: [Seqan-dev] compile problem=0A= =0A= I am getting the following error after a svn checkout (now revision 11686)= =0A= =0A= [ 45%] Building CXX object core/demos/CMakeFiles/sam2svg.dir/sam2svg.cpp.o= =0A= In file included from=0A= /pasteur/solexa2/solexa_travail/PF2/programs/seqan/workspace/seqan/core/dem= os/sam2svg.cpp:8:=0A= /pasteur/solexa2/solexa_travail/PF2/programs/seqan/workspace/seqan/core/inc= lude/seqan/misc/misc_svg.h:124:13:=0A= error: no function template matches function template=0A= specialization 'svgResize'=0A= inline void svgResize(SVGFile &svg, int width, int height)=0A= ^=0A= =0A= Could you please let me know when this is fixed?=0A= =0A= thanks,=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 manuel.holtgrewe@fu-berlin.de Wed Apr 18 14:55:26 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 <1SKUPt-0002ks-S1>; Wed, 18 Apr 2012 14:55:25 +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 <1SKUPt-0006yW-Hn>; Wed, 18 Apr 2012 14:55:25 +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 <1SKUPt-0004j9-Bk>; Wed, 18 Apr 2012 14:55:25 +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 14.02.0283.003; Wed, 18 Apr 2012 14:55:21 +0200 From: "Holtgrewe, Manuel" To: SeqAn Development Thread-Topic: [Seqan-dev] compile problem Thread-Index: AQHNHV9GXfqNeptCxk+kuxZLxe5YK5agiakwgAAAihA= Date: Wed, 18 Apr 2012 12:55:20 +0000 Message-ID: References: <4F8EB43F.6000702@pasteur.fr>, 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: 130.133.170.202 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1334753725-000018DE-8E8175C9/0-0/0-0 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] compile problem 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, 18 Apr 2012 12:55:26 -0000 Ah, it's the vanilla sam2svg demo.= From weese@campus.fu-berlin.de Thu Apr 19 22:37:19 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 <1SKy6Q-0003pH-KI>; Thu, 19 Apr 2012 22:37:18 +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 <1SKy6Q-0007xs-Hq>; Thu, 19 Apr 2012 22:37:18 +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 <1SKy6Q-0006Bd-B8>; Thu, 19 Apr 2012 22:37:18 +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 14.02.0283.003; Thu, 19 Apr 2012 22:37:17 +0200 From: "Weese, David" To: SeqAn Development Thread-Topic: [Seqan-dev] compile problem Thread-Index: AQHNHV9Le0AprUoey0OVNVcUv/gPUZaifCQA Date: Thu, 19 Apr 2012 20:37:16 +0000 Message-ID: <45BD1E80-7F00-495C-B34D-D4C8F584E6A6@fu-berlin.de> References: <4F8EB43F.6000702@pasteur.fr> In-Reply-To: <4F8EB43F.6000702@pasteur.fr> Accept-Language: de-DE, en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: text/plain; charset="iso-8859-1" Content-ID: <42A08B3EE4C3804D8A36333370E841F3@campus.fu-berlin.de> 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::1334867838-000018DE-AA7A52FD/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000348, 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] compile problem 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, 19 Apr 2012 20:37:19 -0000 Fixed. Sorry, that was my fault. David. -- David Weese weese@inf.fu-berlin.de Freie Universit=E4t Berlin http://www.inf.fu-berlin.de/ Institut f=FCr Informatik Phone: +49 30 838 75246 Takustra=DFe 9 Algorithmic Bioinformatics 14195 Berlin Room 021=20 Am 18.04.2012 um 14:31 schrieb Bernd Jagla: > I am getting the following error after a svn checkout (now revision 11686= ) >=20 > [ 45%] Building CXX object core/demos/CMakeFiles/sam2svg.dir/sam2svg.cpp.= o > In file included from /pasteur/solexa2/solexa_travail/PF2/programs/seqan/= workspace/seqan/core/demos/sam2svg.cpp:8: > /pasteur/solexa2/solexa_travail/PF2/programs/seqan/workspace/seqan/core/i= nclude/seqan/misc/misc_svg.h:124:13: error: no function template matches fu= nction template > specialization 'svgResize' > inline void svgResize(SVGFile &svg, int width, int height) > ^ >=20 > Could you please let me know when this is fixed? >=20 > thanks, >=20 > Bernd >=20 >=20 > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev From bernd.jagla@pasteur.fr Fri Apr 20 09:37:38 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 <1SL8PR-0006Hv-BV>; Fri, 20 Apr 2012 09:37:37 +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 <1SL8PR-0006u3-7s>; Fri, 20 Apr 2012 09:37:37 +0200 Received: from maroilles.sis.pasteur.fr (localhost [127.0.0.1]) by mail-interne3.pasteur.fr (Postfix) with ESMTP id B7162381050 for ; Fri, 20 Apr 2012 09:37:35 +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 7D91E381044 for ; Fri, 20 Apr 2012 09:37:35 +0200 (CEST) Message-ID: <4F911236.6040400@pasteur.fr> Date: Fri, 20 Apr 2012 09:37:26 +0200 From: Bernd Jagla User-Agent: Mozilla/5.0 (Windows NT 5.1; rv:11.0) Gecko/20120327 Thunderbird/11.0.1 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::1334907457-000018DE-E0E25640/0-0/0-0 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 X-Spam-Status: No, score=1.4 required=5.0 tests=DNS_FROM_RFC_POST Subject: [Seqan-dev] BZip2 not found 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: