From robf123947@gmail.com Sat Mar 08 19:43:19 2014 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1WMMDO-003SkM-74>; Sat, 08 Mar 2014 19:43:18 +0100 Received: from mail-la0-f65.google.com ([209.85.215.65]) by relay1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1WMMDO-000Brn-4F>; Sat, 08 Mar 2014 19:43:18 +0100 Received: by mail-la0-f65.google.com with SMTP id hr13so1419087lab.4 for ; Sat, 08 Mar 2014 10:43:16 -0800 (PST) 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=VIxzWXo4x0GI/vOwBhNep+gIERDznMXRENrjV0yTQMc=; b=DF2w7Hbv31CkOyf72FV9sitW/yfs8fpJCO+Grd1cYeFYXcUf8RDO2nSzXrG129mFYv mckGi3Xu7vGG1G4vkfUkr8zfkiPaXxpDKTAXw0FGQ9E/paCLwLpQn1uq9+YHZPdgKKiL /NR/hxihJVYVv6cvFRJzgAbD2uAexlyNBxXjDteZhoUK4XVyrBZNHSariq/ss7xmPka7 6DG9yHflNm1ocfF6tLAkVC01Z58W8vFDJxFQnLzHE9sO+ioO1FTVBqN63tCXVa8kZgbY Fur3B43mNy+gLxyTFlbUvxiu+kcp/fcQtQV4Yht4YzKfDK1DXIILDaWPKX8SgDvWjfcU Lq5w== MIME-Version: 1.0 X-Received: by 10.152.29.3 with SMTP id f3mr26446lah.85.1394304196643; Sat, 08 Mar 2014 10:43:16 -0800 (PST) Received: by 10.114.1.225 with HTTP; Sat, 8 Mar 2014 10:43:16 -0800 (PST) Date: Sat, 8 Mar 2014 13:43:16 -0500 Message-ID: From: rob f To: seqan-dev@lists.fu-berlin.de Content-Type: multipart/alternative; boundary=089e0160b6ca598ee604f41cbe8f X-Originating-IP: 209.85.215.65 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1394304198-0000CD40-D65A37A9/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.499994, 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 Algerien.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] different rID values for bam vs. sam with identical data, bam results in assertion failure due to length of namestore 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: Sat, 08 Mar 2014 18:43:19 -0000 --089e0160b6ca598ee604f41cbe8f Content-Type: text/plain; charset=ISO-8859-1 I have a sam and bam file from the same data (an alignment to rn5 refseq genes). Oddly enough I didn't get this error when I aligned to ensembl genes. I am reading the sam/bam files BamStream, but the same error occurs if I drop down to the lower-level Stream approach. I print length(bamStreamIn._nameStore) and each record.rID as it's read in. Here's my output when I use the bam file version of the data: namestore size 42252 record.rID : 10364 record.rID : 41714 record.rID : 20136 record.rID : 5043 ..c/Users/XXXX/shared/seqan-library-1.4.1/include/seqan/bam_io/read_bam.h:208 Assertion failed : static_cast<__uint64>(record.rID) < length(nameStore(context)) was: 43257 >= 42252 Here's the output when I use the sam file: namestore size 42252 record.rID : 10318 record.rID : 41436 record.rID : 20031 record.rID : 5009 record.rID : 13876 record.rID : 12206 ... (output continues successfully until the end of the file) Interestingly the namestore size is the same, but the rIDs are different. Any idea why the rIDs are different and what's causing the assertion error? Thanks -r --089e0160b6ca598ee604f41cbe8f Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
I have a sam and bam file from the same data (an alig= nment to rn5 refseq genes). Oddly enough I didn't get this error when I= aligned to ensembl genes.

I am reading the sam/bam files= BamStream, but the same error occurs if I drop down to the lower-level Str= eam<seqan::Bgzf> approach.

I print length(bamStreamIn._nameStore) and each record.rID as it's = read in. Here's my output when I use the bam file version of the data:<= br>

namestore size 42252
record.rID : 10364
record.rID = : 41714
record.rID : 20136
record.rID : 5043
..c/Users/XXXX/shared/seqan-libr= ary-1.4.1/include/seqan/bam_io/read_bam.h:208 Assertion failed : static_cas= t<__uint64>(record.rID) < length(nameStore(context)) was: 43257 &g= t;=3D 42252

Here's the output when I use the sam file:

namest= ore size 42252
record.rID : 10318
record.rID : 41436
record.rID : = 20031
record.rID : 5009
record.rID : 13876
record.rID : 12206
...
(output continues successfully until the end of the file)

Interestingly the namestore size is the same, but the rIDs are diff= erent. Any idea why the rIDs are different and what's causing the asser= tion error? Thanks

-r
--089e0160b6ca598ee604f41cbe8f-- From robf123947@gmail.com Sat Mar 08 23:24:08 2014 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1WMPf1-003g7i-6m>; Sat, 08 Mar 2014 23:24:03 +0100 Received: from mail-la0-f68.google.com ([209.85.215.68]) by relay1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1WMPf1-000aqb-3p>; Sat, 08 Mar 2014 23:24:03 +0100 Received: by mail-la0-f68.google.com with SMTP id y1so1457171lam.7 for ; Sat, 08 Mar 2014 14:24:01 -0800 (PST) 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=o8oyvP/9YGeTJyxrsQO2LPAzS9YI2f0XqTtipK+stIA=; b=N05vNCG/6hSDXH5s8CjwhvAh7MFtFwe1Uhq2+NBCSW1YLCAEaaiWWmInrmbpd5Aki/ UrEHlupjIl6hDNvna2Ae/F5oLN/0V8omkpbAzw3IMvbl5Vcpb3El4DqWPSLWwOXVdcyY bHabEQAFb7MVKGj9JfXQHdrPebw0qXHz+FiGDW+eDc5XmINBwyTnHQ1xJNUEFNA29gGa LpW8izlZg+jjP6EU4pwFdkg6If/hAeRERkASEbnX56JMHF+qkJUHCvX51ij6N6KNq6A/ /3D4Bc7VEGqIt01xczRFffbdw8yaxT4XicpUW7lOl/VHANBe4EVV0mdVvUqDyMqaEGxB wPMA== MIME-Version: 1.0 X-Received: by 10.112.154.202 with SMTP id vq10mr16553087lbb.3.1394317441511; Sat, 08 Mar 2014 14:24:01 -0800 (PST) Received: by 10.114.1.225 with HTTP; Sat, 8 Mar 2014 14:24:01 -0800 (PST) Date: Sat, 8 Mar 2014 17:24:01 -0500 Message-ID: From: rob f To: seqan-dev@lists.fu-berlin.de Content-Type: multipart/alternative; boundary=089e0112bf44ce35f604f41fd355 X-Originating-IP: 209.85.215.68 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1394317443-0000CD40-702202E1/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.499973, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=0.3 required=5.0 tests=FREEMAIL_FROM, HTML_IMAGE_ONLY_16,HTML_MESSAGE,RCVD_IN_DNSWL_LOW,RCVD_IN_MSPIKE_H3, RCVD_IN_MSPIKE_WL,T_DKIM_INVALID,T_REMOTE_IMAGE X-Spam-Checker-Version: SpamAssassin 3.4.0 on Gabun.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] different rID values for bam vs. sam with identical data, bam results in assertion failure due to length of namestore 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: Sat, 08 Mar 2014 22:24:08 -0000 --089e0112bf44ce35f604f41fd355 Content-Type: text/plain; charset=ISO-8859-1 Hopefully this isn't a duplicate. I didn't see a confirmation in the last email. sorry if it is! I have a sam and bam file from the same data (an alignment to rn5 refseq genes). Oddly enough I didn't get this error when I aligned to ensembl genes. I am reading the sam/bam files BamStream, but the same error occurs if I drop down to the lower-level Stream approach. I print length(bamStreamIn._nameStore) and each record.rID as it's read in. Here's my output when I use the bam file version of the data: namestore size 42252 record.rID : 10364 record.rID : 41714 record.rID : 20136 record.rID : 5043 ..c/Users/XXXX/shared/seqan-library-1.4.1/include/seqan/bam_io/read_bam.h:208 Assertion failed : static_cast<__uint64>(record.rID) < length(nameStore(context)) was: 43257 >= 42252 Here's the output when I use the sam file: namestore size 42252 record.rID : 10318 record.rID : 41436 record.rID : 20031 record.rID : 5009 record.rID : 13876 record.rID : 12206 ... (output continues successfully until the end of the file) Interestingly the namestore size is the same, but the rIDs are different. Any idea why the rIDs are different and what's causing the assertion error? Thanks -r --089e0112bf44ce35f604f41fd355 Content-Type: text/html; charset=ISO-8859-1
Hopefully this isn't a duplicate. I didn't see a confirmation in the last email. sorry if it is!

I have a sam and bam file from the same data (an alignment to rn5 refseq genes). Oddly enough I didn't get this error when I aligned to ensembl genes.

I am reading the sam/bam files BamStream, but the same error occurs if I drop down to the lower-level Stream<seqan::Bgzf> approach.

I print length(bamStreamIn._nameStore) and each record.rID as it's read in. Here's my output when I use the bam file version of the data:

namestore size 42252
record.rID : 10364
record.rID : 41714
record.rID : 20136
record.rID : 5043
..c/Users/XXXX/shared/seqan-library-1.4.1/include/seqan/bam_io/read_bam.h:208 Assertion failed : static_cast<__uint64>(record.rID) < length(nameStore(context)) was: 43257 >= 42252

Here's the output when I use the sam file:

namestore size 42252
record.rID : 10318
record.rID : 41436
record.rID : 20031
record.rID : 5009
record.rID : 13876
record.rID : 12206
...
(output continues successfully until the end of the file)

Interestingly the namestore size is the same, but the rIDs are different. Any idea why the rIDs are different and what's causing the assertion error? Thanks
-r
--089e0112bf44ce35f604f41fd355-- From manuel.holtgrewe@fu-berlin.de Mon Mar 10 09:49:33 2014 Received: from outpost9.zedat.fu-berlin.de ([130.133.4.95]) by list1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1WMvts-001qx5-4j>; Mon, 10 Mar 2014 09:49:32 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1WMvts-0048JT-22>; Mon, 10 Mar 2014 09:49:32 +0100 Received: from cas2.campus.fu-berlin.de ([130.133.170.202]) by relay2.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1WMvtr-0046Uu-0a>; Mon, 10 Mar 2014 09:49:32 +0100 Received: from EX02A.campus.fu-berlin.de ([130.133.170.132]) by CAS2.campus.fu-berlin.de ([130.133.170.202]) with mapi id 14.03.0174.001; Mon, 10 Mar 2014 09:49:30 +0100 From: "Holtgrewe, Manuel" To: SeqAn Development Thread-Topic: [Seqan-dev] different rID values for bam vs. sam with identical data, bam results in assertion failure due to length of namestore Thread-Index: AQHPOx0iOzSYrfWB/0m/upd5NHULcpraBODU 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_FCCAB9D80C3DAB47B5601C5B0E62872B9618B7C2ex02acampusfube_" MIME-Version: 1.0 Date: Mon, 10 Mar 2014 09:49:28 +0100 X-Original-Date: Mon, 10 Mar 2014 08:49:28 +0000 X-Originating-IP: 130.133.170.202 X-ZEDAT-Hint: XA X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1394441372-0000CD40-A40D8D1B/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.464296, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-50.0 required=5.0 tests=ALL_TRUSTED,HTML_MESSAGE X-Spam-Checker-Version: SpamAssassin 3.4.0 on Benin.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] different rID values for bam vs. sam with identical data, bam results in assertion failure due to length of namestore 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, 10 Mar 2014 08:49:33 -0000 --_000_FCCAB9D80C3DAB47B5601C5B0E62872B9618B7C2ex02acampusfube_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi Rob, can you send us a minimal example, i.e. the SAM file with the header and th= e offending record and its conversion to BAM and a small demo program? Thanks, Manuel ________________________________ From: rob f [robf123947@gmail.com] Sent: Saturday, March 08, 2014 11:24 PM To: seqan-dev@lists.fu-berlin.de Subject: [Seqan-dev] different rID values for bam vs. sam with identical da= ta, bam results in assertion failure due to length of namestore Hopefully this isn't a duplicate. I didn't see a confirmation in the last e= mail. sorry if it is! I have a sam and bam file from the same data (an alignment to rn5 refseq ge= nes). Oddly enough I didn't get this error when I aligned to ensembl genes. I am reading the sam/bam files BamStream, but the same error occurs if I dr= op down to the lower-level Stream approach. I print length(bamStreamIn._nameStore) and each record.rID as it's read in.= Here's my output when I use the bam file version of the data: namestore size 42252 record.rID : 10364 record.rID : 41714 record.rID : 20136 record.rID : 5043 ..c/Users/XXXX/shared/seqan-library-1.4.1/include/seqan/bam_io/read_bam.h:2= 08 Assertion failed : static_cast<__uint64>(record.rID) < length(nameStore(= context)) was: 43257 >=3D 42252 Here's the output when I use the sam file: namestore size 42252 record.rID : 10318 record.rID : 41436 record.rID : 20031 record.rID : 5009 record.rID : 13876 record.rID : 12206 ... (output continues successfully until the end of the file) Interestingly the namestore size is the same, but the rIDs are different. A= ny idea why the rIDs are different and what's causing the assertion error? = Thanks [https://mail.google.com/mail/images/cleardot.gif] -r --_000_FCCAB9D80C3DAB47B5601C5B0E62872B9618B7C2ex02acampusfube_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi Rob,

can you send us a minimal example, i.e. the SAM file with the header a= nd the offending record and its conversion to BAM and a small demo program?=

Thanks,
Manuel

From: rob f [robf123947@gmail.com]
Sent: Saturday, March 08, 2014 11:24 PM
To: seqan-dev@lists.fu-berlin.de
Subject: [Seqan-dev] different rID values for bam vs. sam with ident= ical data, bam results in assertion failure due to length of namestore

Hopefully this isn't a duplicate. I didn't see a confirmat= ion in the last email. sorry if it is!

I have a sam and bam file from the same data (an alignment to rn5 refs= eq genes). Oddly enough I didn't get this error when I aligned to ensembl g= enes.

I am reading the sam/bam files BamStream, but the same error occurs if= I drop down to the lower-level Stream<seqan::Bgzf> approach.

I print length(bamStreamIn._nameStore) and each record.rID as it's read in.= Here's my output when I use the bam file version of the data:

namestore size 42252
record.rID : 10364
record.rID : 41714
record.rID : 20136
record.rID : 5043
..c/Users/XXXX/shared/seqan-library-1.4.1/include/seqan/bam_io/read_bam.h:2= 08 Assertion failed : static_cast<__uint64>(record.rID) < length(n= ameStore(context)) was: 43257 >=3D 42252

Here's the output when I use the sam file:

namestore size 42252
record.rID : 10318
record.rID : 41436
record.rID : 20031
record.rID : 5009
record.rID : 13876
record.rID : 12206
...
(output continues successfully until the end of the file)

Interestingly the namestore size is the same, but the rIDs are different. A= ny idea why the rIDs are different and what's causing the assertion error? = Thanks
-r