From matthias.dodt@mdc-berlin.de Thu Dec 02 15:57:13 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 <1POAat-0007Tz-VB>; Thu, 02 Dec 2010 15:57:12 +0100 Received: from smtp2.bbbm.mdc-berlin.de ([141.80.25.21]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1POAat-0005Hn-M5>; Thu, 02 Dec 2010 15:57:11 +0100 Received: from localhost (localhost [127.0.0.1]) by smtp2.bbbm.mdc-berlin.de (Postfix) with ESMTP id 642073A28C for ; Thu, 2 Dec 2010 15:57:11 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:subject:subject:mime-version :user-agent:from:from:date:date:message-id:received:received :received:received; s=dkim1; t=1291301824; x=1293116224; bh=j6ll 7pOhnffKE7QXUPyvGreutn0RhDnTV0/XCsUZcmk=; b=r6pg1oqvZ5q9HZy/Pbvp uuuQ4tlsRKKWIQ0uHa45wvZtl7aDy0AuEFOhnimDVvqnPv6yvHGjsYu9Ck6DYLgh oXaU8dpBHd3U3iCcCWyeyweQ9q1MukqJPP0WxcOBBZjsaL4i8nTY9iVq4PB7Ky4Y lVcYGfdQkDT0ccUFJRxDUWk= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from smtp2.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (smtp2.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id Esmf42gGyfDC for ; Thu, 2 Dec 2010 15:57:04 +0100 (CET) Received: from mdcmail.mdc-berlin.de (mab.citx.mdc-berlin.de [141.80.36.102]) by smtp2.bbbm.mdc-berlin.de (Postfix) with ESMTP for ; Thu, 2 Dec 2010 15:57:04 +0100 (CET) Received: from mdcexcl.mdc-berlin.net ([141.80.184.16]) by mdcmail.mdc-berlin.de with Microsoft SMTPSVC(6.0.3790.4675); Thu, 2 Dec 2010 15:58:08 +0100 Received: from cd04-macpro.local ([141.80.188.98]) by mdcexcl.mdc-berlin.net with Microsoft SMTPSVC(6.0.3790.4675); Thu, 2 Dec 2010 15:58:01 +0100 Message-ID: <4CF7B413.6000707@mdc-berlin.de> Date: Thu, 02 Dec 2010 15:58:27 +0100 From: Mat User-Agent: Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.5; de; rv:1.9.2.12) Gecko/20101027 Lightning/1.0b2 Thunderbird/3.1.6 MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de Content-Type: multipart/alternative; boundary="------------060700000709060203070504" X-OriginalArrivalTime: 02 Dec 2010 14:58:01.0873 (UTC) FILETIME=[50E99810:01CB9231] X-TM-AS-Product-Ver: SMEX-10.0.0.1412-6.500.1024-17802.007 X-TM-AS-Result: No--5.919500-0.000000-31 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-Originating-IP: 141.80.25.21 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1291301831-00000C0F-217F1068/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.029312, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Gabun.ZEDAT.-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.9 required=5.0 tests=HTML_50_60,HTML_MESSAGE, RATWARE_GECKO_BUILD Subject: [Seqan-dev] mason problem 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, 02 Dec 2010 14:57:13 -0000 This is a multi-part message in MIME format. --------------060700000709060203070504 Content-Type: text/plain; charset=ISO-8859-15; format=flowed Content-Transfer-Encoding: 7bit Hi there! I got a problem with mason for 454 read simulation. The command was: mason 454 -sq -mp E_tenella.fasta (Eimeria tenella genome) The error message: .... contig # 2148/4707 contig # 2149/4707 contig # 2150/4707 contig # 2151/4707 contig # 2152/4707 contig # 2153/4707 /home/mat/seqan/seqan-trunk/projects/library/seqan/sequence_journaled/journal_entries_sorted_array.h:394 Assertion failed : it->virtualPosition >= delta was: 216739043537519363 < 18230286505148746552 Aborted Any suggestions? Thanks! best, mat --------------060700000709060203070504 Content-Type: text/html; charset=ISO-8859-15 Content-Transfer-Encoding: 8bit Hi there!

I got a problem with mason for 454 read simulation. The command was:

mason 454 -sq -mp E_tenella.fasta

(Eimeria tenella genome)

The error message:
....
    contig # 2148/4707
    contig # 2149/4707
    contig # 2150/4707
    contig # 2151/4707
    contig # 2152/4707
    contig # 2153/4707
/home/mat/seqan/seqan-trunk/projects/library/seqan/sequence_journaled/journal_entries_sorted_array.h:394 Assertion failed : it->virtualPosition >= delta was: 216739043537519363 < 18230286505148746552
Aborted

Any suggestions?

Thanks!

best,

mat
 --------------060700000709060203070504-- From manuel.holtgrewe@fu-berlin.de Thu Dec 02 20:27:34 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 <1POEoW-0000m6-Mm>; Thu, 02 Dec 2010 20:27:32 +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 <1POEoW-00076y-Kd>; Thu, 02 Dec 2010 20:27:32 +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 <1POEoW-0004qZ-FT>; Thu, 02 Dec 2010 20:27:32 +0100 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by exchange6.fu-berlin.de ([160.45.9.133]) with mapi; Thu, 2 Dec 2010 20:27:32 +0100 From: "Holtgrewe, Manuel" To: SeqAn Development Date: Thu, 2 Dec 2010 20:27:29 +0100 Thread-Topic: [Seqan-dev] mason problem Thread-Index: AcuSVvbxMIrnWMg+Qt6HXgaqxfgXiw== Message-ID: References: <4CF7B413.6000707@mdc-berlin.de> In-Reply-To: <4CF7B413.6000707@mdc-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: multipart/alternative; boundary="_000_E57B5D957F564F7F97306A22A30FEF51fuberlinde_" MIME-Version: 1.0 X-Originating-IP: 160.45.9.133 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1291318052-00000C0F-EF42836F/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000016, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Benin.ZEDAT.-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] mason problem 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, 02 Dec 2010 19:27:34 -0000 --_000_E57B5D957F564F7F97306A22A30FEF51fuberlinde_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Can you send me the E_tenella.fasta file? The list will probably block atta= chements... On Dec 2, 2010, at 3:58 PM, Mat wrote: Hi there! I got a problem with mason for 454 read simulation. The command was: mason 454 -sq -mp E_tenella.fasta (Eimeria tenella genome) The error message: .... contig # 2148/4707 contig # 2149/4707 contig # 2150/4707 contig # 2151/4707 contig # 2152/4707 contig # 2153/4707 /home/mat/seqan/seqan-trunk/projects/library/seqan/sequence_journaled/journ= al_entries_sorted_array.h:394 Assertion failed : it->virtualPosition >=3D d= elta was: 216739043537519363 < 18230286505148746552 Aborted Any suggestions? Thanks! best, mat --_000_E57B5D957F564F7F97306A22A30FEF51fuberlinde_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Can you send me the E_tene= lla.fasta file? The list will probably block attachements...

<= div>On Dec 2, 2010, at 3:58 PM, Mat wrote:

Hi there!

I got a problem with mason for 454 read simulation. The command was:

mason 454 -sq -mp E_tenella.fasta

(Eimeria tenella genome)

The error message:
....
    contig # 2148/4707
    contig # 2149/4707
    contig # 2150/4707
    contig # 2151/4707
    contig # 2152/4707
    contig # 2153/4707
/home/mat/seqan/seqan-trunk/projects/library/seqan/sequence_journaled= /journal_entries_sorted_array.h:394 Assertion failed : it->virtualPosition >=3D delta was: 216739043537519363 < 18230286505148746552
Aborted

Any suggestions?

Thanks!

best,

mat
<ATT00001..txt>

= --_000_E57B5D957F564F7F97306A22A30FEF51fuberlinde_-- From manuel.holtgrewe@fu-berlin.de Mon Dec 06 17:34:20 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 <1PPe15-0000Ss-8s>; Mon, 06 Dec 2010 17:34:19 +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 <1PPe15-0001E1-78>; Mon, 06 Dec 2010 17:34:19 +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 <1PPe15-0004lB-1a>; Mon, 06 Dec 2010 17:34:19 +0100 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by exchange6.fu-berlin.de ([160.45.9.133]) with mapi; Mon, 6 Dec 2010 17:34:19 +0100 From: "Holtgrewe, Manuel" To: SeqAn Development Date: Mon, 6 Dec 2010 17:34:17 +0100 Thread-Topic: [Seqan-dev] mason problem Thread-Index: AcuVY22jRDNlSgo9Rm2A2esmxWuRlw== Message-ID: References: <4CF7B413.6000707@mdc-berlin.de> In-Reply-To: <4CF7B413.6000707@mdc-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-type: clean X-purgate-ID: 151147::1291653259-00000C0F-726E75EC/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.-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: Re: [Seqan-dev] mason problem 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, 06 Dec 2010 16:34:20 -0000 r8279 should fix this problem. The issue was deletion of characters in the haplotype behind the actual end= . HTH *m Am 02.12.2010 um 15:58 schrieb Mat: > Hi there! >=20 > I got a problem with mason for 454 read simulation. The command was: >=20 > mason 454 -sq -mp E_tenella.fasta >=20 > (Eimeria tenella genome) >=20 > The error message: > .... > contig # 2148/4707 > contig # 2149/4707 > contig # 2150/4707 > contig # 2151/4707 > contig # 2152/4707 > contig # 2153/4707 > /home/mat/seqan/seqan-trunk/projects/library/seqan/sequence_journaled/jou= rnal_entries_sorted_array.h:394 Assertion failed : it->virtualPosition >=3D= delta was: 216739043537519363 < 18230286505148746552 > Aborted >=20 > Any suggestions? >=20 > Thanks! >=20 > best, >=20 > mat > From matthias.dodt@mdc-berlin.de Tue Dec 07 11:23:25 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 <1PPuhf-0000sD-1u>; Tue, 07 Dec 2010 11:23:23 +0100 Received: from sinope.bbbm.mdc-berlin.de ([141.80.25.23]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1PPuhe-0006Fi-VB>; Tue, 07 Dec 2010 11:23:23 +0100 Received: from localhost (localhost [127.0.0.1]) by sinope.bbbm.mdc-berlin.de (Postfix) with ESMTP id 8445517C8C9 for ; Tue, 7 Dec 2010 11:23:22 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:in-reply-to:references:subject:subject :mime-version:user-agent:from:from:date:date:message-id:received :received:received:received; s=dkim1; t=1291717395; x= 1293531795; bh=uS54l8VHc33czr4AiI/9YOSsoIT3BIxdAxpF4YgXsok=; b=q 1h3YvuY/hT9CfH2gpzpz2xd9Rt4klF5+/UxVaYc7NVjq1sg32Kl3we8JY1G9n6FC rbpGZex4NapMPfXY/ttUb1XFDuBNjf8w6N2vH6yqre7lxAOWLMWFVD3YqZESvqPz RENAczaCrTak4UKBvg29YuB+Em3+jiUCBDuqFe7N/M= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from sinope.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (sinope.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id HdOxrDhIC+bu for ; Tue, 7 Dec 2010 11:23:15 +0100 (CET) Received: from mdcmail.mdc-berlin.de (mab.citx.mdc-berlin.de [141.80.36.102]) by sinope.bbbm.mdc-berlin.de (Postfix) with ESMTP for ; Tue, 7 Dec 2010 11:23:15 +0100 (CET) Received: from mdcexcl.mdc-berlin.net ([141.80.184.16]) by mdcmail.mdc-berlin.de with Microsoft SMTPSVC(6.0.3790.4675); Tue, 7 Dec 2010 11:24:01 +0100 Received: from cd04-macpro.local ([141.80.188.98]) by mdcexcl.mdc-berlin.net with Microsoft SMTPSVC(6.0.3790.4675); Tue, 7 Dec 2010 11:24:01 +0100 Message-ID: <4CFE0B61.3070700@mdc-berlin.de> Date: Tue, 07 Dec 2010 11:24:33 +0100 From: Mat User-Agent: Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.5; de; rv:1.9.2.12) Gecko/20101027 Lightning/1.0b2 Thunderbird/3.1.6 MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de References: <4CF7B413.6000707@mdc-berlin.de> In-Reply-To: Content-Type: multipart/alternative; boundary="------------050008050000040505000707" X-OriginalArrivalTime: 07 Dec 2010 10:24:01.0086 (UTC) FILETIME=[DD8155E0:01CB95F8] X-TM-AS-Product-Ver: SMEX-10.0.0.1412-6.500.1024-17814.000 X-TM-AS-Result: No--13.611700-0.000000-31 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-Originating-IP: 141.80.25.23 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1291717403-00000C0F-424387C5/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000044, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Gabun.ZEDAT.-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=1.0 required=5.0 tests=HTML_40_50,HTML_MESSAGE, HTML_TITLE_EMPTY,RATWARE_GECKO_BUILD Subject: Re: [Seqan-dev] mason problem 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: Tue, 07 Dec 2010 10:23:25 -0000 This is a multi-part message in MIME format. --------------050008050000040505000707 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Excellent! Now it works- Thanks! Best, mat Am 12/6/10 5:34 PM, schrieb Holtgrewe, Manuel: > r8279 should fix this problem. > > The issue was deletion of characters in the haplotype behind the actual end. > > HTH > *m > > Am 02.12.2010 um 15:58 schrieb Mat: > >> Hi there! >> >> I got a problem with mason for 454 read simulation. The command was: >> >> mason 454 -sq -mp E_tenella.fasta >> >> (Eimeria tenella genome) >> >> The error message: >> .... >> contig # 2148/4707 >> contig # 2149/4707 >> contig # 2150/4707 >> contig # 2151/4707 >> contig # 2152/4707 >> contig # 2153/4707 >> /home/mat/seqan/seqan-trunk/projects/library/seqan/sequence_journaled/journal_entries_sorted_array.h:394 Assertion failed : it->virtualPosition>= delta was: 216739043537519363< 18230286505148746552 >> Aborted >> >> Any suggestions? >> >> Thanks! >> >> best, >> >> mat >> > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev --------------050008050000040505000707 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Excellent! Now it works-

Thanks!

Best,

mat

Am 12/6/10 5:34 PM, schrieb Holtgrewe, Manuel: 
r8279 should fix this problem.

The issue was deletion of characters in the haplotype behind the actual end.

HTH
*m

Am 02.12.2010 um 15:58 schrieb Mat:


Hi there!

I got a problem with mason for 454 read simulation. The command was:

mason 454 -sq -mp E_tenella.fasta

(Eimeria tenella genome)

The error message:
....
    contig # 2148/4707
    contig # 2149/4707
    contig # 2150/4707
    contig # 2151/4707
    contig # 2152/4707
    contig # 2153/4707
/home/mat/seqan/seqan-trunk/projects/library/seqan/sequence_journaled/journal_entries_sorted_array.h:394 Assertion failed : it->virtualPosition >= delta was: 216739043537519363 < 18230286505148746552
Aborted

Any suggestions?

Thanks!

best,

mat
<ATT00001..txt>


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--------------050008050000040505000707-- From matthias.dodt@mdc-berlin.de Tue Dec 07 11:53:35 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 <1PPvAs-0001qP-FJ>; Tue, 07 Dec 2010 11:53:34 +0100 Received: from sinope.bbbm.mdc-berlin.de ([141.80.25.23]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1PPvAs-00017R-CF>; Tue, 07 Dec 2010 11:53:34 +0100 Received: from localhost (localhost [127.0.0.1]) by sinope.bbbm.mdc-berlin.de (Postfix) with ESMTP id ED0AA17C8A9 for ; Tue, 7 Dec 2010 11:53:33 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:subject:subject:mime-version :user-agent:from:from:date:date:message-id:received:received :received:received; s=dkim1; t=1291719208; x=1293533608; bh=Etf3 cpIPihGMBY4WG+vGe2FZsFquhvp0XOHGpsLZaMM=; b=W7anu7nSOD7e6QZ4MjSA LZ7f7U+6mKm2B/90ThfXN7UktF1NCMIFYF6Ize4fRsYxQLrnwnjrF9kcZY25324A oeqVAmxaimQCz+TE1APaVtb7Jn4ms9fMb9dlA8y3ZXpVsVX4V0JmTZihJ6HVxBb9 1yWP2m57BzfrdZD/lZSsGz0= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from sinope.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (sinope.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id ilj1hLEso1wt for ; Tue, 7 Dec 2010 11:53:28 +0100 (CET) Received: from mdcmail.mdc-berlin.de (mab.citx.mdc-berlin.de [141.80.36.102]) by sinope.bbbm.mdc-berlin.de (Postfix) with ESMTP for ; Tue, 7 Dec 2010 11:53:28 +0100 (CET) Received: from mdcexcl.mdc-berlin.net ([141.80.184.16]) by mdcmail.mdc-berlin.de with Microsoft SMTPSVC(6.0.3790.4675); Tue, 7 Dec 2010 11:52:59 +0100 Received: from cd04-macpro.local ([141.80.188.98]) by mdcexcl.mdc-berlin.net with Microsoft SMTPSVC(6.0.3790.4675); Tue, 7 Dec 2010 11:52:58 +0100 Message-ID: <4CFE122A.1060600@mdc-berlin.de> Date: Tue, 07 Dec 2010 11:53:30 +0100 From: Mat User-Agent: Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.5; de; rv:1.9.2.12) Gecko/20101027 Lightning/1.0b2 Thunderbird/3.1.6 MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de Content-Type: multipart/alternative; boundary="------------070905050906070402060202" X-OriginalArrivalTime: 07 Dec 2010 10:52:58.0818 (UTC) FILETIME=[E9463220:01CB95FC] X-TM-AS-Product-Ver: SMEX-10.0.0.1412-6.500.1024-17814.000 X-TM-AS-Result: No--11.580500-0.000000-31 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-Originating-IP: 141.80.25.23 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1291719214-00000C0F-3647515B/0-0/0-0 X-Bogosity: Unsure, tests=bogofilter, spamicity=0.461071, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Gabun.ZEDAT.-Berlin.DE X-Spam-Level: xx X-Spam-Status: No, score=2.4 required=5.0 tests=FU_BOGO_UNSURE,HTML_40_50, HTML_MESSAGE,RATWARE_GECKO_BUILD Subject: [Seqan-dev] finding mates in fragment store 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: Tue, 07 Dec 2010 10:53:35 -0000 This is a multi-part message in MIME format. --------------070905050906070402060202 Content-Type: text/plain; charset=ISO-8859-15; format=flowed Content-Transfer-Encoding: 7bit Hi Guys! I am loading a SAM file into a fragment store and would like to enter all the reads which have a mate into a graph, if the mate's were aligned to different contigs. I am not sure how to search the FragmentStore for a certain read id. I got: ... unsigned int nrAlignments = length(fragStore.alignedReadStore),mateCounter=0; for (unsigned int n=0;n>> the Fragment store is not indexed by the read_id... std::cout << "read-id: " << fragStore.alignedReadStore[mate_id].readId << std::endl; std::cout << "pair-id: " << fragStore.alignedReadStore[mate_id].pairMatchId << std::endl; std::cout << "contig-id: " << fragStore.alignedReadStore[mate_id].contigId << std::endl; <<<< //ceck if congtig-ids are unequal... //insert into graph... break; } } ... Thanks! Best, mat --------------070905050906070402060202 Content-Type: text/html; charset=ISO-8859-15 Content-Transfer-Encoding: 8bit Hi Guys!

I am loading a SAM file into a fragment store and would like to enter all the reads which have a mate into a graph, if the mate's were aligned to different contigs. I am not sure how to search the FragmentStore for a certain read id. I got:

...
    unsigned int nrAlignments = length(fragStore.alignedReadStore),mateCounter=0;

    for (unsigned int n=0;n<nrAlignments;++n){

        unsigned int mate_id = fragStore.alignedReadStore[n].pairMatchId;

        if(mate_id!=TReadStoreElement::INVALID_ID){
            ++mateCounter;
            std::cout << "read-id: " << n << ","<<fragStore.alignedReadStore[n].readId << std::endl;
            std::cout << "pair-id: " << fragStore.alignedReadStore[n].pairMatchId << std::endl;
            std::cout << "contig-id: " << fragStore.alignedReadStore[n].contigId << std::endl;

            //get mate contig-id

>>> the Fragment store is not indexed by the read_id...
            std::cout << "read-id: " << fragStore.alignedReadStore[mate_id].readId << std::endl;
            std::cout << "pair-id: " << fragStore.alignedReadStore[mate_id].pairMatchId << std::endl;
            std::cout << "contig-id: " << fragStore.alignedReadStore[mate_id].contigId << std::endl;
<<<<

            //ceck if congtig-ids are unequal...

            //insert into graph...
            break;
        }
    }
...

Thanks!

Best,

mat
 --------------070905050906070402060202-- From manuel.holtgrewe@fu-berlin.de Mon Dec 20 15:26:08 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 <1PUggg-0006nK-Gc>; Mon, 20 Dec 2010 15:26:06 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.69) with esmtp (envelope-from ) id <1PUggg-0000SA-E4>; Mon, 20 Dec 2010 15:26:06 +0100 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by relay2.zedat.fu-berlin.de (Exim 4.69) with esmtp (envelope-from ) id <1PUggg-0003My-89>; Mon, 20 Dec 2010 15:26:06 +0100 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by exchange6.fu-berlin.de ([160.45.9.133]) with mapi; Mon, 20 Dec 2010 15:26:06 +0100 From: "Holtgrewe, Manuel" To: SeqAn Development Date: Mon, 20 Dec 2010 15:27:57 +0100 Thread-Topic: Line ending style changes Thread-Index: AcugUdYOriSvI5btRjeAHxOA8OAkYA== Message-ID: <299598C3-4564-417A-8543-4438DAD432D4@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: multipart/alternative; boundary="_000_299598C34564417A85434438DAD432D4fuberlinde_" MIME-Version: 1.0 X-Originating-IP: 160.45.9.133 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1292855166-00000C13-F2687A45/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000010, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Dschibuti.ZEDAT.-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED,HTML_30_40, HTML_MESSAGE Subject: [Seqan-dev] Line ending style changes 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, 20 Dec 2010 14:26:08 -0000 --_000_299598C34564417A85434438DAD432D4fuberlinde_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Dear all, we are currently performing some large-scale changes in the Seqan codebase = trunk. This includes line style changes. All text files have their svn:eol-style p= roperty set to native now. This means when checking them out, you will get = "\r\n" on Windows and "\n" on unices. This hopefully circumvents some probl= em with line ending consitencies (e.g. you open a file with Unix line endin= gs on Windows with Visual Studio which makes newly inserted line endings Wi= ndows line endings. If you have local changes, you might get conflicts when updating. We hope t= his will not cause too many inconveniences. However, the step has to be tak= en sooner or later for the better and the later we do this the more harm it= will do. More information can be found in the SeAn Wiki and Subversion manual http://trac.mi.fu-berlin.de/seqan/wiki/HowTo/UseNativeLineEndings http://svnbook.red-bean.com/en/1.1/ch07s02.html Bests, Manuel --_000_299598C34564417A85434438DAD432D4fuberlinde_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Dear all,

we are currently performing some large-scale changes in the Seqan codeba= se trunk.

This includes line style changes. All te= xt files have their svn:eol-style property set to native now. This means wh= en checking them out, you will get "\r\n" on Windows and "\n" on unices. Th= is hopefully circumvents some problem with line ending consitencies (e.g. y= ou open a file with Unix line endings on Windows with Visual Studio which m= akes newly inserted line endings Windows line endings.

=
If you have local changes, you might get conflicts when updating. We h= ope this will not cause too many inconveniences. However, the step has to b= e taken sooner or later for the better and the later we do this the more ha= rm it will do.

More information can be found in th= e SeAn Wiki and Subversion manual


Bests,
Man= uel
= --_000_299598C34564417A85434438DAD432D4fuberlinde_-- From Knut.Reinert@fu-berlin.de Tue Dec 21 22:24:12 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 <1PV9go-0006OC-TA>; Tue, 21 Dec 2010 22:24:11 +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 <1PV9go-0003Dr-QT>; Tue, 21 Dec 2010 22:24:10 +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 <1PV9go-0000Tu-Jr>; Tue, 21 Dec 2010 22:24:10 +0100 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by exchange6.fu-berlin.de ([160.45.9.133]) with mapi; Tue, 21 Dec 2010 22:24:10 +0100 From: "Reinert, Knut" To: "seqan-dev@lists.fu-berlin.de" Importance: low X-Priority: 5 Date: Tue, 21 Dec 2010 22:24:08 +0100 Thread-Topic: SeqAn Version 1.3 (RC1) in SVN and downloadable Thread-Index: AcuhVWg7UlzXWGR8Sdqk0Vw0Erzsug== Message-ID: Accept-Language: en-US, de-DE Content-Language: de-DE X-MS-Has-Attach: yes X-MS-TNEF-Correlator: user-agent: Microsoft-MacOutlook/14.1.0.101012 acceptlanguage: en-US, de-DE Content-Type: multipart/signed; protocol="application/pkcs7-signature"; micalg=sha1; boundary="B_3375815048_11093981" MIME-Version: 1.0 X-Originating-IP: 160.45.9.133 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1292966650-00000C13-85445633/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000057, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Algerien.ZEDAT.-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-1.8 required=5.0 tests=ALL_TRUSTED,HTML_MESSAGE, TO_ADDRESS_EQ_REAL,USERPASS Subject: [Seqan-dev] SeqAn Version 1.3 (RC1) in SVN and downloadable 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: Tue, 21 Dec 2010 21:24:12 -0000 --B_3375815048_11093981 Content-type: multipart/alternative; boundary="B_3375815048_11090104" --B_3375815048_11090104 Content-type: text/plain; charset="ISO-8859-1" Content-transfer-encoding: quoted-printable Dear SeqAn users, The SeqAn team is pleased to announce release 1.3(rc1) of the SeqAn C++ library. Please find details about the content and new features under http:://www.seqan.de We wish you a happy holiday season, The SeqAn team ----------------------------------------------------------------------- Prof. Dr.-Ing. Knut Reinert Phone/fax : +49 30 838 75 222/218 Algorithmic Bioinformatics Mobile : +49 160 7195754 Freie Universit=E4t Berlin Skype : knut.reinert Takustrasse 9 E-Mail: reinert@inf.fu-berlin.de D-14195 Berlin, Germany Web : http://knut.reinert.ws ------------------------------------------------------------------------ --B_3375815048_11090104 Content-type: text/html; charset="ISO-8859-1" Content-transfer-encoding: quoted-printable
Dear SeqAn users,

The SeqAn team is pleased to announce release 1.3(rc1) = of the SeqAn C++ library.

Please find details about the content and new features under 
http:://www.seqan.de

We wish you a happy holiday= season,

The SeqAn team

=
--------------------------------------= ---------------------------------
Prof. Dr.-Ing. Knut Reinert  =       Phone/fax  : +49 30 838 75 222/218
Algorithmic Bio= informatics         Mobile : +49 160 7195754
Freie Universit=E4= t Berlin           Skype : knut.reinert
Takustrasse 9  &= nbsp;            = ;       E-Mail: = reinert@inf.fu-be= rlin.de
D-14195 Berlin, Germany    &nb= sp;       Web     : http://knut.rein= ert.ws
-----------------------------------------------------------------= -------

=

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