From jwillis0720@gmail.com Wed Apr 08 07:47:19 2015 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Yfipa-003EEs-28>; Wed, 08 Apr 2015 07:47:18 +0200 Received: from mail-pd0-f179.google.com ([209.85.192.179]) by relay1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1YfipZ-003wKn-Re>; Wed, 08 Apr 2015 07:47:18 +0200 Received: by pdea3 with SMTP id a3so103759153pde.3 for ; Tue, 07 Apr 2015 22:47:15 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=from:content-type:content-transfer-encoding:subject:message-id:date :to:mime-version; bh=g5OZJw1e8BM434N6C5Mu6YfSwZSNIO2rrow2HkUuXdc=; b=e92n2Kgk/bTAAdhzkw9CGyxHRE8YanFd+Nc3Rot4Ml3eDpQaxszBM8tOlnBIEWbFaA /VRHJtaFeKKA/xOyPG+o0hJ5IXpK+U5oxkMI96imJVn2CbYLTFnOy6zqvbtGzovuyxlC 1s9kSlL5oW1k7GfqEUNIlWwH2hFQOZVdmUoJa4yqlEkPgh5bI2mGAgOSFRzTH5o6GlRY frTx5sAsGbozUORJt4MmzwG5YpqtcUg0tuUaV9583A8oxdRxwcEaxjUCO2/OEi8ojg+R IsmrMze5OX3Dah8DcREFEzAUzOLXJKNkSNmeK76PrVmTWGZB8f5+AlBbrQZ2iQbyhgv1 kD6w== X-Received: by 10.66.62.137 with SMTP id y9mr43443942par.87.1428472034816; Tue, 07 Apr 2015 22:47:14 -0700 (PDT) Received: from [192.168.0.13] (cpe-76-167-196-136.san.res.rr.com. [76.167.196.136]) by mx.google.com with ESMTPSA id vl9sm8425053pbc.73.2015.04.07.22.47.12 for (version=TLSv1 cipher=ECDHE-RSA-RC4-SHA bits=128/128); Tue, 07 Apr 2015 22:47:13 -0700 (PDT) From: Jordan Willis Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: quoted-printable Message-Id: <7CC82BB1-6634-4CB9-925E-CCA0F59FB4CB@gmail.com> Date: Tue, 7 Apr 2015 22:47:11 -0700 To: seqan-dev@lists.fu-berlin.de Mime-Version: 1.0 (Mac OS X Mail 8.2 \(2070.6\)) X-Mailer: Apple Mail (2.2070.6) X-Originating-IP: 209.85.192.179 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1428472038-00000DE8-DF0B6BA6/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.497514, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-0.7 required=5.0 tests=FREEMAIL_FROM, RCVD_IN_DNSWL_LOW,RCVD_IN_MSPIKE_H2,T_DKIM_INVALID X-Spam-Checker-Version: SpamAssassin 3.4.0 on Palau.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] c++11 and Mavericks generates sem_destroy warning X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 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, 08 Apr 2015 05:47:19 -0000 Hay anyone else come across this? The only thing I think is different = was switching to Mavericks, but I get this warning. include/seqan/system/system_sema.h:110:24: warning: 'sem_destroy' is = deprecated [-Wdeprecated-declarations] bool res =3D sem_destroy(hSemaphore); ^ /usr/include/sys/semaphore.h:53:5: note: 'sem_destroy' has been = explicitly marked deprecated here int sem_destroy(sem_t *) __deprecated; Jordan= From Enrico.Siragusa@fu-berlin.de Thu Apr 09 11:36:10 2015 Received: from outpost9.zedat.fu-berlin.de ([130.133.4.95]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Yg8sa-0013z7-R1>; Thu, 09 Apr 2015 11:36:08 +0200 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Yg8sa-000oqO-Q5>; Thu, 09 Apr 2015 11:36:08 +0200 Received: from cas1.campus.fu-berlin.de ([130.133.170.201]) by relay2.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1Yg8sa-002kzo-Lq>; Thu, 09 Apr 2015 11:36:08 +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 14.03.0224.002; Thu, 9 Apr 2015 11:36:07 +0200 From: "Siragusa, Enrico" To: SeqAn Development Thread-Topic: [Seqan-dev] c++11 and Mavericks generates sem_destroy warning Thread-Index: AQHQcb+JQoZ17+JnvE2zGQZop/jolp1ES/AA Message-ID: <1FD9EE1D-AB70-4C26-BA7C-A8C1C7AE77FE@fu-berlin.de> References: <7CC82BB1-6634-4CB9-925E-CCA0F59FB4CB@gmail.com> In-Reply-To: <7CC82BB1-6634-4CB9-925E-CCA0F59FB4CB@gmail.com> Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: text/plain; charset="us-ascii" Content-ID: <12E040829BF5FD4385239987AE5981DC@campus.fu-berlin.de> Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 Date: Thu, 09 Apr 2015 11:36:05 +0200 X-Original-Date: Thu, 9 Apr 2015 09:36:05 +0000 X-Originating-IP: 130.133.170.201 X-ZEDAT-Hint: X X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1428572168-00000DE8-776CBB89/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-50.0 required=5.0 tests=ALL_TRUSTED X-Spam-Checker-Version: SpamAssassin 3.4.0 on Niue.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] c++11 and Mavericks generates sem_destroy warning X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 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, 09 Apr 2015 09:36:10 -0000 Dear Jordan, Please update to SeqAn 2.0.0 if you want to get rid of this warning. Thanks, Enrico On 08 Apr 2015, at 07:47, Jordan Willis wrote: > Hay anyone else come across this? The only thing I think is different was= switching to Mavericks, but I get this warning. >=20 > include/seqan/system/system_sema.h:110:24: warning: 'sem_destroy' is depr= ecated > [-Wdeprecated-declarations] > bool res =3D sem_destroy(hSemaphore); > ^ > /usr/include/sys/semaphore.h:53:5: note: 'sem_destroy' has been explicitl= y marked deprecated here > int sem_destroy(sem_t *) __deprecated; >=20 >=20 > Jordan > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev From zhaoyanswill@gmail.com Mon Apr 20 05:17:04 2015 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Yk2Cl-003DSW-27>; Mon, 20 Apr 2015 05:17:03 +0200 Received: from mail-ie0-f180.google.com ([209.85.223.180]) by relay1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1Yk2Ck-002fNG-Si>; Mon, 20 Apr 2015 05:17:03 +0200 Received: by iejt8 with SMTP id t8so107224192iej.2 for ; Sun, 19 Apr 2015 20:17:00 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=message-id:date:from:user-agent:mime-version:to:subject :content-type:content-transfer-encoding; bh=XaVInEFbuqxlM0Sqmus4Yyml430GuAkRME/sQZUmYy4=; b=uE9jAFlmWMrstsIcjEqPMjvvGTfnbwzCOKqZ0gRQX/5fawnnrRKT0NoM1m3s5lN81N zPh18gkureNm+CUy2Y85+cDEfmghQ6T5ev69bZ0/VY4XjIx/nB60ILb40vyywBrB/Lxl fdkQHPHtx8MPHdYMFOJCV8A4AAEC0ayX4Cy+GO68XBJhMF7J7j63duPaQG+BsbNkNQ66 DPDGh+PpMHjKvYA7O3l3WQ4FYloX+2ncVbt25j2I46+yHKnKzpuBIZ++BUcCoB/LuVUX +jguk1w6ctLHqbBcV3/FrlucEuj5j9zx4cT9Qu4L3s7CkqTS5qfbWKlUlROonTkuE0Or uT6w== X-Received: by 10.107.136.25 with SMTP id k25mr18464430iod.88.1429499820077; Sun, 19 Apr 2015 20:17:00 -0700 (PDT) Received: from [192.168.1.3] (c-68-51-126-113.hsd1.in.comcast.net. [68.51.126.113]) by mx.google.com with ESMTPSA id j2sm10844751ioi.8.2015.04.19.20.16.59 for (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128/128); Sun, 19 Apr 2015 20:16:59 -0700 (PDT) Message-ID: <55346FAB.3070108@gmail.com> Date: Sun, 19 Apr 2015 23:16:59 -0400 From: Y Z User-Agent: Mozilla/5.0 (Windows NT 6.3; WOW64; rv:31.0) Gecko/20100101 Thunderbird/31.6.0 MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 7bit X-Originating-IP: 209.85.223.180 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1429499823-00000DE8-494B1CFE/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.163548, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-1.4 required=5.0 tests=FREEMAIL_FROM, RCVD_IN_DNSWL_LOW,RCVD_IN_MSPIKE_H2,T_DKIM_INVALID X-Spam-Checker-Version: SpamAssassin 3.4.0 on Vanuatu.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] building BWT error X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 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 Apr 2015 03:17:04 -0000 Dear whom may concern, I followed the Mini Botie tutorial to build a BWT index for human genome reference (hg38). TIndex fmIndex(text); TIter it(fmIndex); search(it, fragStore.readSeqStore); save(fmIndex, ...); However, after about 570 minutes, the program crashed with the message: Asynchronous I/O operation failed (waitFor with timeOut=0ms) "Success" fildes: 4 ".../include/seqan/file/file_page.h:842 FAILED! (writing operation could not be completed: "Success") Could you give me some suggestions about the error? The time building the index is much longer than what I expected. Is there anything wrong in my code? Thanks a lot! -- Sincerely, Yongan From hannes.hauswedell@fu-berlin.de Mon Apr 20 12:41:01 2015 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Yk98N-003xOS-KH>; Mon, 20 Apr 2015 12:40:59 +0200 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Yk98N-0033wn-JJ>; Mon, 20 Apr 2015 12:40:59 +0200 Received: from celegans.imp.fu-berlin.de ([160.45.111.134]) by inpost2.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtpsa (envelope-from ) id <1Yk98N-002c12-IK>; Mon, 20 Apr 2015 12:40:59 +0200 From: Hannes Hauswedell To: seqan-dev@lists.fu-berlin.de Date: Mon, 20 Apr 2015 12:42:19 +0200 Message-ID: <2960999.4x0C7q4Rqf@celegans.imp.fu-berlin.de> Organization: MPI MolGen / FU-Berlin In-Reply-To: <55346FAB.3070108@gmail.com> References: <55346FAB.3070108@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" X-Originating-IP: 160.45.111.134 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1429526459-00000DE8-F6AEED08/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-50.0 required=5.0 tests=ALL_TRUSTED, T_FILL_THIS_FORM_SHORT X-Spam-Checker-Version: SpamAssassin 3.4.0 on Kiribati.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] building BWT error X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 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 Apr 2015 10:41:01 -0000 Am Sonntag, 19. April 2015, 23:16:59 schrieb Y Z: > Dear whom may concern, >=20 > I followed the Mini Botie tutorial to build a BWT index for human gen= ome > reference (hg38). > TIndex fmIndex(text); > TIter it(fmIndex); > search(it, fragStore.readSeqStore); > save(fmIndex, ...); >=20 > However, after about 570 minutes, the program crashed with the messag= e: > Asynchronous I/O operation failed (waitFor with timeOut=3D0ms) "Succe= ss" > fildes: 4 > ".../include/seqan/file/file_page.h:842 FAILED! (writing operation co= uld > not be completed: "Success") This is an indicator for you running out of space in your temporary dir= ectory.=20 You can change your temporary directory by setting the TMPDIR environme= nt=20 variable! Hope that helps, --=20 Hannes Hauswedell PhD student Max Planck Institute for Molecular Genetics / Freie Universit=C3=A4t Be= rlin address Institut f=C3=BCr Informatik Takustra=C3=9Fe 9 Room 019 14195 Berlin telephone +49 (0)30 838-75241 fax +49 (0)30 838-75218 e-mail hannes.hauswedell@[molgen.mpg.de|fu-berlin.de] From dubarry.ma@gmail.com Tue Apr 21 12:46:19 2015 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1YkVh4-003CJN-35>; Tue, 21 Apr 2015 12:46:18 +0200 Received: from mail-wi0-f176.google.com ([209.85.212.176]) by relay1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1YkVh4-003u7Z-0b>; Tue, 21 Apr 2015 12:46:18 +0200 Received: by widdi4 with SMTP id di4so16570025wid.0 for ; Tue, 21 Apr 2015 03:46:16 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:date:message-id:subject:from:to:content-type; bh=+DPbkRX9AZ3ehQ4/jsUos8wjlHXSPqRNz7wWH+UsR6w=; b=KDDxOh6nQw1/32KvvFyJODuF+ifpIXrSpgn0bRWnT+DWSK0xOCpbnEH0QpnWPvjROC GqhoDpvorbeu0O9Y7m5Lxa/MB49Q0BsOIGqpbO0FIBuM7vFd3M5fY7Ybvw5Vi6gpEEM3 4w8IyUImuPlEFifdZlx2APg2kO9MqiOmDOhivWfoBSc7fbhhkIaH9evYT03uOQNjFwkW GmiLgVmkqeq6Vy1KmOHp8gP3pIL3GLh5L7BJ7J+R/P2e9qbbIVYKVaBllSnS1pOE96xs Q+AtSLYS+BAibSmtsTnCAGUMP+WDnRx25VHmYHZk1OotXVCcaa4rvDIgoorzkhFJHaUo 57uw== MIME-Version: 1.0 X-Received: by 10.180.100.194 with SMTP id fa2mr31531508wib.8.1429613176406; Tue, 21 Apr 2015 03:46:16 -0700 (PDT) Received: by 10.194.79.71 with HTTP; Tue, 21 Apr 2015 03:46:16 -0700 (PDT) Date: Tue, 21 Apr 2015 12:46:16 +0200 Message-ID: From: marion dubarry To: seqan-dev@lists.fu-berlin.de Content-Type: multipart/alternative; boundary=f46d0444ed398bc5d7051439c18f X-Originating-IP: 209.85.212.176 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1429613178-00000DE8-C0FD4E73/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.002401, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-0.7 required=5.0 tests=FREEMAIL_FROM,HTML_MESSAGE, RCVD_IN_DNSWL_LOW,RCVD_IN_MSPIKE_H3,RCVD_IN_MSPIKE_WL,T_DKIM_INVALID X-Spam-Checker-Version: SpamAssassin 3.4.0 on Niue.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] problem to use BamRecordToAlignment X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 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 Apr 2015 10:46:19 -0000 --f46d0444ed398bc5d7051439c18f Content-Type: text/plain; charset=UTF-8 Hello, I think I have a basic question, sorry in advance. I don't understand what is suppose to contain "references" of a record from the methods BamRecordToAlignment(). Reference is suppose to contain : "The string with the reference that record lies on." I start with the example and I modify it : BamAlignmentRecord record; StringSet references; Align align; while (!atEnd(bamFileIn)) { readRecord(record, bamFileIn); appendValue(references,record.seq); if (record.rID != BamAlignmentRecord::INVALID_REFID) bamRecordToAlignment(align, references[record.rID], record); } I try a lot of think for the variable "references", this is my last try. Because references is of type Dna5String. I try a lot of things (most of time absurd things) and I obtain always this error : seqan-src/include/seqan/sequence/string_base.h:429 Assertion failed : static_cast(pos) < static_cast(length(me)) was: 1 >= 1 (Trying to access an element behind the last one!) Aborted (core dumped) I think the problem come from my variable references, could you explain me what is it suppose to contain ? Thanks, Sorry for my (stupid) question, Marion --f46d0444ed398bc5d7051439c18f Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hello,

I think I hav= e a basic question, sorry in advance. I don't understand what is suppos= e to contain "references" of a record from the methods BamRecordT= oAlignment().
Reference is suppose to contain : "The string with the reference that record lies on= ."
I start with the example and I modify it :

=C2=A0 BamA= lignmentRecord record;
=C2=A0 StringSet<Dna5String> references;=C2=A0 Align<Dna5String> align;
=C2=A0 while (!atEnd(bamFileIn))<= br>=C2=A0 {
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 readRecord(record= , bamFileIn);
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 appendValue(ref= erences,record.seq);

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 if (record= .rID !=3D BamAlignmentRecord::INVALID_REFID)
=C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0=C2=A0 bamRecordToAlignment(align, references[record.r= ID], record);
=C2=A0=C2=A0=C2=A0 }

I try a lot of think for= the variable "references", this is my last try. Because referenc= es is of type Dna5String. I try a lot of things (most of time absurd things= ) and I obtain always this error :
seqan-src/include/seqan/sequence/stri= ng_base.h:429 Assertion failed : static_cast<TStringPos>(pos) < st= atic_cast<TStringPos>(length(me)) was: 1 >=3D 1 (Trying to access = an element behind the last one!)
Aborted (core dumped)

I think the problem come from my variable references, could you explain me= what is it suppose to contain ?

Thanks,
Sorry = for my (stupid) question,
Marion
--f46d0444ed398bc5d7051439c18f-- From jwillis0720@gmail.com Tue Apr 21 12:57:46 2015 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1YkVs8-003G8T-AP>; Tue, 21 Apr 2015 12:57:44 +0200 Received: from mail-yk0-f175.google.com ([209.85.160.175]) by relay1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1YkVs8-003xff-4p>; Tue, 21 Apr 2015 12:57:44 +0200 Received: by ykep21 with SMTP id p21so21974055yke.3 for ; Tue, 21 Apr 2015 03:57:41 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=from:content-type:message-id:mime-version:subject:date:references :to:in-reply-to; bh=tO39gxbwmBBirWdKfHdTUB8Cr3QdZZFEv+voZiUkVwg=; b=rl+LckmLqkJCvxjBB64kaGnodUFgTFJIYQIcGZV/FsishcgopdJmS5/SZiJwjmGtWP M4t4CrXr3MCpmx6yAewB/m40f//Lc3K6ONzOn/F9t/YesDy1VJpbv+5As2PYhy3HB7B3 iHjf/a2ozaNWrg0eph3wch3Dbw26yR73f5sQQLOz6hwuFDrGL2Huhi1OrrbkwPQlcW8K NW909L40SuuCkBQRIzA6X1g6UrWvLlDNl+Wc4FObxlV0JF9DnsiLmZLYM6XInlqtiCUu M4/Gaw3zksqKdsU9akuDlPrdUKLX1lnIaScVd2oCPnnQfd6MOPoXwqVNk0ITSNVmIQeo /+eg== X-Received: by 10.236.53.161 with SMTP id g21mr16591968yhc.23.1429613861239; Tue, 21 Apr 2015 03:57:41 -0700 (PDT) Received: from [10.2.243.62] ([129.59.115.2]) by mx.google.com with ESMTPSA id l66sm1149473yha.2.2015.04.21.03.57.39 for (version=TLSv1 cipher=ECDHE-RSA-RC4-SHA bits=128/128); Tue, 21 Apr 2015 03:57:40 -0700 (PDT) From: Jordan Willis Content-Type: multipart/alternative; boundary="Apple-Mail=_69B6A437-19DE-48EA-9A59-6D5473339874" Message-Id: Mime-Version: 1.0 (Mac OS X Mail 8.2 \(2070.6\)) Date: Tue, 21 Apr 2015 03:57:38 -0700 References: To: SeqAn Development In-Reply-To: X-Mailer: Apple Mail (2.2070.6) X-Originating-IP: 209.85.160.175 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1429613864-00000DE8-01675CD1/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.054566, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-1.0 required=5.0 tests=FREEMAIL_FROM,HTML_MESSAGE, RCVD_IN_DNSWL_LOW,RCVD_IN_MSPIKE_H2,T_DKIM_INVALID X-Spam-Checker-Version: SpamAssassin 3.4.0 on Kiribati.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] problem to use BamRecordToAlignment X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 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 Apr 2015 10:57:46 -0000 --Apple-Mail=_69B6A437-19DE-48EA-9A59-6D5473339874 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Hi, Where is you bamFileIn defined? > On Apr 21, 2015, at 3:46 AM, marion dubarry = wrote: >=20 > Hello, >=20 > I think I have a basic question, sorry in advance. I don't understand = what is suppose to contain "references" of a record from the methods = BamRecordToAlignment(). > Reference is suppose to contain : "The string with the reference that = record lies on." > I start with the example and I modify it :=20 >=20 > BamAlignmentRecord record; > StringSet references; > Align align; > while (!atEnd(bamFileIn)) > { > readRecord(record, bamFileIn); > appendValue(references,record.seq); >=20 > if (record.rID !=3D BamAlignmentRecord::INVALID_REFID) > bamRecordToAlignment(align, references[record.rID], = record); > } >=20 > I try a lot of think for the variable "references", this is my last = try. Because references is of type Dna5String. I try a lot of things = (most of time absurd things) and I obtain always this error : > seqan-src/include/seqan/sequence/string_base.h:429 Assertion failed : = static_cast(pos) < static_cast(length(me)) was: = 1 >=3D 1 (Trying to access an element behind the last one!) > Aborted (core dumped) >=20 > I think the problem come from my variable references, could you = explain me what is it suppose to contain ?=20 >=20 > Thanks, > Sorry for my (stupid) question, > Marion > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev --Apple-Mail=_69B6A437-19DE-48EA-9A59-6D5473339874 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=us-ascii Hi,

Where = is you bamFileIn defined?



On = Apr 21, 2015, at 3:46 AM, marion dubarry <dubarry.ma@gmail.com> wrote:

Hello,

I = think I have a basic question, sorry in advance. I don't understand what = is suppose to contain "references" of a record from the methods = BamRecordToAlignment().
Reference is = suppose to contain : "The string with = the reference that record lies on."
I start = with the example and I modify it :

  = BamAlignmentRecord record;
  = StringSet<Dna5String> references;
  = Align<Dna5String> align;
  while = (!atEnd(bamFileIn))
  {
        readRecord(record, = bamFileIn);
        = appendValue(references,record.seq);

       if (record.rID !=3D = BamAlignmentRecord::INVALID_REFID)
      =          bamRecordToAlignment(align, = references[record.rID], record);
    }

I try a lot of think for the variable = "references", this is my last try. Because references is of type = Dna5String. I try a lot of things (most of time absurd things) and I = obtain always this error :
seqan-src/include/seqan/sequence/string_base.h:429 Assertion = failed : static_cast<TStringPos>(pos) < = static_cast<TStringPos>(length(me)) was: 1 >=3D 1 (Trying to = access an element behind the last one!)
Aborted (core = dumped)

I think the = problem come from my variable references, could you explain me what is = it suppose to contain ?

Thanks,
Sorry for my (stupid) = question,
Marion
_______________________________________________
seqan-dev = mailing list
seqan-dev@lists.fu-berlin.de
https://lists.fu-berlin.de/listinfo/seqan-dev

= --Apple-Mail=_69B6A437-19DE-48EA-9A59-6D5473339874-- From dubarry.ma@gmail.com Tue Apr 21 13:03:46 2015 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1YkVxw-003IyV-DK>; Tue, 21 Apr 2015 13:03:44 +0200 Received: from mail-wg0-f44.google.com ([74.125.82.44]) by relay1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1YkVxw-003zrq-BU>; Tue, 21 Apr 2015 13:03:44 +0200 Received: by wgsk9 with SMTP id k9so208933457wgs.3 for ; Tue, 21 Apr 2015 04:03:43 -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=25ge8lz+7TGeqBm5GkouHRUln9220N2lqHPpmHWOESE=; b=0wilUxVagAIxZ8VoaEUJt1+0wtkyDTKy6Z8x7QAJKe3tradGpOGqX3632eaQK4TZWX FVTiXw/JdboLW+to1igrhQsw4uUIzW99Uq2u+pojyDJOLhZ5z6DisSS1VaS7kJF13hN5 qVucNxH0ppllYAcmaZYBM0Fct7Ncqq05uw+rdPw0TUifpjcR0yjfFa0ptvG0y2ZTf044 Z4Y01zlY2WWTDxDq8lUthtjOZ3DOJsyvuhD/+/BfGKKuJ/5vT0icATjFlnHPqXoV0ylj IHA+CNZ49tfvhQor00M+tsvgXXt2PXncY7heRFAKd70GeXeprgkaYueqHo/fak8KFOgD 5NfQ== MIME-Version: 1.0 X-Received: by 10.194.133.102 with SMTP id pb6mr39109812wjb.97.1429614223040; Tue, 21 Apr 2015 04:03:43 -0700 (PDT) Received: by 10.194.79.71 with HTTP; Tue, 21 Apr 2015 04:03:42 -0700 (PDT) In-Reply-To: References: Date: Tue, 21 Apr 2015 13:03:42 +0200 Message-ID: From: marion dubarry To: SeqAn Development Content-Type: multipart/alternative; boundary=089e012292eeee2656051439ffba X-Originating-IP: 74.125.82.44 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1429614224-00000DE8-7A6101EA/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-0.7 required=5.0 tests=FREEMAIL_FROM,HTML_MESSAGE, RCVD_IN_DNSWL_LOW,RCVD_IN_MSPIKE_H3,RCVD_IN_MSPIKE_WL,T_DKIM_INVALID X-Spam-Checker-Version: SpamAssassin 3.4.0 on Palau.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] problem to use BamRecordToAlignment X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 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 Apr 2015 11:03:46 -0000 --089e012292eeee2656051439ffba Content-Type: text/plain; charset=UTF-8 BamFileIn bamFileIn; if (!open(bamFileIn,File.c_str())){ cout << "Error : Cannot open " << File << endl; exit(1); } I don't think this is the error because I can read the headers, or the records. Just the bamRecordToAlignment() function fail 2015-04-21 12:57 GMT+02:00 Jordan Willis : > Hi, > > Where is you bamFileIn defined? > > > > On Apr 21, 2015, at 3:46 AM, marion dubarry wrote: > > Hello, > > I think I have a basic question, sorry in advance. I don't understand what > is suppose to contain "references" of a record from the methods > BamRecordToAlignment(). > Reference is suppose to contain : "The string with the reference that > record lies on." > I start with the example and I modify it : > > BamAlignmentRecord record; > StringSet references; > Align align; > while (!atEnd(bamFileIn)) > { > readRecord(record, bamFileIn); > appendValue(references,record.seq); > > if (record.rID != BamAlignmentRecord::INVALID_REFID) > bamRecordToAlignment(align, references[record.rID], record); > } > > I try a lot of think for the variable "references", this is my last try. > Because references is of type Dna5String. I try a lot of things (most of > time absurd things) and I obtain always this error : > seqan-src/include/seqan/sequence/string_base.h:429 Assertion failed : > static_cast(pos) < static_cast(length(me)) was: 1 > >= 1 (Trying to access an element behind the last one!) > Aborted (core dumped) > > I think the problem come from my variable references, could you explain me > what is it suppose to contain ? > > Thanks, > Sorry for my (stupid) question, > Marion > _______________________________________________ > 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 > > --089e012292eeee2656051439ffba Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
BamFileIn bamFileIn;
=C2=A0=C2=A0=C2=A0 if (!open(= bamFileIn,File.c_str())){
=C2=A0=C2=A0=C2=A0 =C2=A0=C2=A0=C2=A0 cout <= ;< "Error : Cannot open " << File << endl;
=C2= =A0=C2=A0=C2=A0 =C2=A0=C2=A0=C2=A0 exit(1);
=C2=A0=C2=A0=C2=A0 }

=
I don't think this is the error because I can read the headers, o= r the records. Just the bamRecordToAlignment() function fail

2015-04-21 12:57 GMT+0= 2:00 Jordan Willis <jwillis0720@gmail.com>:
Hi,

Where is you bamFileIn defined?



On Apr 21= , 2015, at 3:46 AM, marion dubarry <dubarry.ma@gmail.com> wrote:

H= ello,

I think I have a basic question, sorry in advance. I don= 't understand what is suppose to contain "references" of a re= cord from the methods BamRecordToAlignment().
Reference is su= ppose to contain : "The string with the refere= nce that record lies on."
I start with the example and I= modify it :

=C2=A0 BamAlignmentRecord record;
=C2=A0 StringSet&= lt;Dna5String> references;
=C2=A0 Align<Dna5String> align;
= =C2=A0 while (!atEnd(bamFileIn))
=C2=A0 {
=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0 readRecord(record, bamFileIn);
=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0 appendValue(references,record.seq);

=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0 if (record.rID !=3D BamAlignmentRecord::INVALID_RE= FID)
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 bamRecordToA= lignment(align, references[record.rID], record);
=C2=A0=C2=A0=C2=A0 }
I try a lot of think for the variable "references", th= is is my last try. Because references is of type Dna5String. I try a lot of= things (most of time absurd things) and I obtain always this error :
se= qan-src/include/seqan/sequence/string_base.h:429 Assertion failed : static_= cast<TStringPos>(pos) < static_cast<TStringPos>(length(me)) = was: 1 >=3D 1 (Trying to access an element behind the last one!)
Abor= ted (core dumped)

I think the problem come from my variab= le references, could you explain me what is it suppose to contain ?
Thanks,
Sorry for my (stupid) question,
Mario= n
_______________________________________________
seqan-dev mailing listseqan-d= ev@lists.fu-berlin.de
https://lists.fu-berlin.de/listinfo/seqan-dev=


______________________= _________________________
seqan-dev mailing list
seqan-dev@lists.fu-berlin.d= e
https://lists.fu-berlin.de/listinfo/seqan-dev


--089e012292eeee2656051439ffba--