From manuel.holtgrewe@fu-berlin.de Mon Mar 01 16:23:27 2010 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 <1Nm7Sw-00087z-Ic>; Mon, 01 Mar 2010 16:23:26 +0100 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 <1Nm7Sw-0002oc-G6>; Mon, 01 Mar 2010 16:23:26 +0100 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by relay2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Nm7Sw-0001Zb-CK>; Mon, 01 Mar 2010 16:23:26 +0100 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by exchange6.fu-berlin.de ([160.45.9.133]) with mapi; Mon, 1 Mar 2010 16:23:26 +0100 From: "Holtgrewe, Manuel" To: "seqan-dev@lists.fu-berlin.de" Date: Mon, 1 Mar 2010 16:23:25 +0100 Thread-Topic: [Seqan-dev] trac still working? Thread-Index: Acq5UyNMZDGWZe49SL6fDpdxWqAY+w== Message-ID: <91EB1355-56B1-462D-A335-55AE80F8B4D1@fu-berlin.de> Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: acceptlanguage: en-US, de-DE Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Originating-IP: 160.45.9.133 X-purgate: clean X-purgate-ID: 151147::1267457006-00000DDD-15500F4C/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.204828, version=1.1.6 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Botsuana.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.4 required=5.0 tests=ALL_TRUSTED, TO_ADDRESS_EQ_REAL Subject: Re: [Seqan-dev] trac still working? X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 01 Mar 2010 15:23:27 -0000 John, I am sorry that we have not fixed the bugs you reported yet. Because of the life cycle of PhD student in academica, we had a little lack= of man power for developing in SeqAn. Hopefully, things will improve now t= hat another PhD student and I have started working on SeqAn.=20 Please continue to use Trac to submit errors. Actually, we are in the proce= ss of embracing Trac usage further. Also keep in mind that while we try our best to improve the library all the= time, we have other projects and deadlines to take care of. However, there= will be a week or so in the second quarter of 2010 when we will focus on a= nalyzing and fixing all known issues. As for the spam, I'm looking into removing it. Bests, Manuel= From j.reid@mail.cryst.bbk.ac.uk Thu Mar 04 12:09:17 2010 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 <1Nn8vb-0004zD-T8>; Thu, 04 Mar 2010 12:09:15 +0100 Received: from adora-ext.cryst.bbk.ac.uk ([193.61.32.13] helo=adora.cryst.bbk.ac.uk) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Nn8vb-00073D-PH>; Thu, 04 Mar 2010 12:09:15 +0100 Received: from [127.0.0.1] (axon-ext.cryst.bbk.ac.uk [193.61.32.77]) by adora.cryst.bbk.ac.uk (8.13.8/8.13.8) with ESMTP id o24BAGsO014653 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NO) for ; Thu, 4 Mar 2010 11:10:17 GMT Message-ID: <4B8F94D5.3090808@mail.cryst.bbk.ac.uk> Date: Thu, 04 Mar 2010 11:09:09 +0000 From: John Reid User-Agent: Thunderbird 2.0.0.23 (X11/20090817) MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de References: In-Reply-To: Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit X-Cryst-BBK-MailScanner-Information: Please contact CCSG for more information (http://www. cryst.bbk.ac.uk/CCSG) X-Cryst-BBK-MailScanner-ID: o24BAGsO014653 X-Cryst-BBK-MailScanner: Found to be clean X-Cryst-BBK-MailScanner-SpamCheck: not spam, SpamAssassin (not cached, score=1.673, required 5, HTML_MESSAGE 0.00, MIME_HTML_ONLY 1.67) X-Cryst-BBK-MailScanner-SpamScore: s X-Cryst-BBK-MailScanner-From: j.reid@mail.cryst.bbk.ac.uk X-Cryst-BBK-MailScanner-Watermark: 1268305819.17617@mn+RF94fi+PlWrFVJ4NZOQ X-Originating-IP: 193.61.32.13 X-purgate: clean X-purgate-ID: 151147::1267700955-00000DDD-498BD857/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.025862, version=1.1.6 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Botsuana.ZEDAT.FU-Berlin.DE X-Spam-Level: x X-Spam-Status: No, score=1.8 required=5.0 tests=DNS_FROM_RFC_ABUSE, HTML_60_70, HTML_MESSAGE,HTML_TAG_EXIST_TBODY,MIME_HTML_ONLY,SPF_HELO_PASS, SPF_PASS Subject: Re: [Seqan-dev] trac still working? X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 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 Mar 2010 11:09:17 -0000

seqan-dev-request@lists.fu-berlin.de wrote:

Subject:
Re: [Seqan-dev] trac still working?
From:
"Holtgrewe, Manuel" <manuel.holtgrewe@fu-berlin.de>
Date:
Mon, 1 Mar 2010 16:23:25 +0100
To:
"seqan-dev@lists.fu-berlin.de" <seqan-dev@lists.fu-berlin.de>
To:
"seqan-dev@lists.fu-berlin.de" <seqan-dev@lists.fu-berlin.de>		 

John,

I am sorry that we have not fixed the bugs you reported yet.

Because of the life cycle of PhD student in academica, we had a little lack of man power for developing in SeqAn. Hopefully, things will improve now that another PhD student and I have started working on SeqAn.
Great sounds good.
Please continue to use Trac to submit errors. Actually, we are in the process of embracing Trac usage further.
Will do if I find any.
Also keep in mind that while we try our best to improve the library all the time, we have other projects and deadlines to take care of. However, there will be a week or so in the second quarter of 2010 when we will focus on analyzing and fixing all known issues.
I understand that there are no guarantees that if or when bugs will be fixed in free open-source projects. I just wanted to know whether there is active development or support of seqan and that my bug reports were visible to those who might be interested in them.
As for the spam, I'm looking into removing it.
That would be great.


Thanks again,
John.
From aaronquinlan@gmail.com Mon Mar 22 15:13:37 2010 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 <1NtiNr-0007hH-0S>; Mon, 22 Mar 2010 15:13:35 +0100 Received: from mail-vw0-f54.google.com ([209.85.212.54]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1NtiNq-00026M-Qc>; Mon, 22 Mar 2010 15:13:34 +0100 Received: by vws1 with SMTP id 1so388228vws.13 for ; Mon, 22 Mar 2010 07:13:33 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=gamma; h=domainkey-signature:received:received:from:content-type :content-transfer-encoding:subject:date:message-id:to:mime-version :x-mailer; bh=dD3h6Bhj96L9bBehL0aILQde8NuvqspSt+FOY027/2g=; b=GW5bzIZ5EWo5KyiFkoY3Xm8nV9CR2riF87839CFerP1rE68m0QGbS7dXP9kBMaT67O Zk81+7MYRtbLK5VN+u6qVr7SzkNQIGF/0fkzrtvClRLbw4VFcO0u1kKXBtAISS4PPlJX y3qp92iBy8L25ltV9UkBwes8CtnXiIcx+Wiv8= DomainKey-Signature: a=rsa-sha1; c=nofws; d=gmail.com; s=gamma; h=from:content-type:content-transfer-encoding:subject:date:message-id :to:mime-version:x-mailer; b=WVEN0MuovGanAgZ/Pr5ptgGioYcS+Yt7Lu4hQOow+/n+k64yGEsKEYCgz7cThFnzoI Vo/Zwd6c8FDReC4Tm8fJbO4h4qROhNE6Z2DtGC/lELOpCBN9wKQrSkcc0+0TVW0vBU16 IbPgcXKg/e6to0zrN3IIT6ceNZzy5XpPcLQS4= Received: by 10.220.124.232 with SMTP id v40mr17107vcr.36.1269267213104; Mon, 22 Mar 2010 07:13:33 -0700 (PDT) Received: from qbm.bioch.virginia.edu (qbm.bioch.Virginia.EDU [128.143.16.77]) by mx.google.com with ESMTPS id 33sm35588629vws.10.2010.03.22.07.13.31 (version=TLSv1/SSLv3 cipher=RC4-MD5); Mon, 22 Mar 2010 07:13:32 -0700 (PDT) From: Aaron Quinlan Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: quoted-printable Date: Mon, 22 Mar 2010 10:13:30 -0400 Message-Id: To: seqan-dev@lists.fu-berlin.de Mime-Version: 1.0 (Apple Message framework v1077) X-Mailer: Apple Mail (2.1077) X-Originating-IP: 209.85.212.54 X-purgate: clean X-purgate-ID: 151147::1269267215-00000DDD-4CC0C704/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.045620, version=1.1.6 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, RCVD_BY_IP, SPF_HELO_PASS,SPF_PASS Subject: [Seqan-dev] createQGramIndex example X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 22 Mar 2010 14:13:37 -0000 Hi all, =20 I would like to use SeqAn to create a qgram/kmer index of the mouse = genome and would like to have control over the kmer and step sizes. I = have tried combined bits of example code on the website to do this, but = either cannot get it compile or cause segfaults. =20 Is there a clear working example (perhaps I've missed it) of creating = a qgram index from a genome StringSet and then using it to seed = alignments from say a FASTQ file? That said, as has been noted in an earlier post to this list, I find = that the readMeta function does not work with FASTQ. What idiom should = be followed for extracting ids, sequences and qualities from a FASTQ = file? All the best and thanks for creating this library...I think once I can = get rolling it will be incredibly useful and powerful. Best, Aaron Quinlan University of Virginia=