From unknown Sun Aug 17 09:10:32 2025 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Mailer: MIME-tools 5.509 (Entity 5.509) Content-Type: text/plain; charset=utf-8 From: bug#15206 <15206@debbugs.gnu.org> To: bug#15206 <15206@debbugs.gnu.org> Subject: Status: Report od bugs Reply-To: bug#15206 <15206@debbugs.gnu.org> Date: Sun, 17 Aug 2025 16:10:32 +0000 retitle 15206 Report od bugs reassign 15206 coreutils submitter 15206 Kaitao Lai severity 15206 normal tag 15206 notabug thanks From debbugs-submit-bounces@debbugs.gnu.org Thu Aug 29 02:15:02 2013 Received: (at submit) by debbugs.gnu.org; 29 Aug 2013 06:15:02 +0000 Received: from localhost ([127.0.0.1]:34937 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.80) (envelope-from ) id 1VEvVV-0003qw-1w for submit@debbugs.gnu.org; Thu, 29 Aug 2013 02:15:01 -0400 Received: from eggs.gnu.org ([208.118.235.92]:34097) by debbugs.gnu.org with esmtp (Exim 4.80) (envelope-from ) id 1VEvIq-0003Xm-DR for submit@debbugs.gnu.org; Thu, 29 Aug 2013 02:01:57 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1VEvIg-0004jH-7J for submit@debbugs.gnu.org; Thu, 29 Aug 2013 02:01:56 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: ** X-Spam-Status: No, score=2.8 required=5.0 tests=BAYES_50,DEAR_SOMETHING, HTML_MESSAGE autolearn=disabled version=3.3.2 Received: from lists.gnu.org ([2001:4830:134:3::11]:58791) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1VEvIg-0004jD-5B for submit@debbugs.gnu.org; Thu, 29 Aug 2013 02:01:46 -0400 Received: from eggs.gnu.org ([2001:4830:134:3::10]:35767) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1VEvIX-0002oN-Lz for bug-coreutils@gnu.org; Thu, 29 Aug 2013 02:01:46 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1VEvIO-0004h5-Sr for bug-coreutils@gnu.org; Thu, 29 Aug 2013 02:01:37 -0400 Received: from mailhub1.soe.uq.edu.au ([130.102.132.208]:53121 helo=newmailhub.uq.edu.au) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1VEvIO-0004gV-9B for bug-coreutils@gnu.org; Thu, 29 Aug 2013 02:01:28 -0400 Received: from smtp2.soe.uq.edu.au (smtp2.soe.uq.edu.au [10.138.113.41]) by newmailhub.uq.edu.au (8.14.5/8.14.5) with ESMTP id r7T61LkF012356 for ; Thu, 29 Aug 2013 16:01:22 +1000 Received: from UQEXET1.soe.uq.edu.au (uqexet1.soe.uq.edu.au [130.102.129.38]) by smtp2.soe.uq.edu.au (8.14.5/8.14.5) with ESMTP id r7T61Ld5030547 (version=TLSv1/SSLv3 cipher=AES128-SHA bits=128 verify=NOT) for ; Thu, 29 Aug 2013 16:01:21 +1000 Received: from uqexht3.soe.uq.edu.au (130.102.129.72) by UQEXET1.soe.uq.edu.au (130.102.129.38) with Microsoft SMTP Server (TLS) id 14.1.355.2; Thu, 29 Aug 2013 16:01:21 +1000 Received: from uqexmdb8.soe.uq.edu.au ([169.254.8.12]) by uqexht3.soe.uq.edu.au ([130.102.129.72]) with mapi id 14.01.0355.002; Thu, 29 Aug 2013 16:01:21 +1000 From: Kaitao Lai To: "bug-coreutils@gnu.org" Subject: Report od bugs Thread-Topic: Report od bugs Thread-Index: Ac6kfDIEMNmz0w1UTGiGaumuBTEnFA== Date: Thu, 29 Aug 2013 06:01:20 +0000 Message-ID: Accept-Language: en-AU, en-US Content-Language: zh-CN X-MS-Has-Attach: X-MS-TNEF-Correlator: x-originating-ip: [172.18.13.86] Content-Type: multipart/alternative; boundary="_000_E65DA92157873943BE52B62F964A934D0F30CAA7uqexmdb8soeuqed_" MIME-Version: 1.0 X-UQ-FilterTime: 1377756082 X-Scanned-By: MIMEDefang 2.73 on UQ Mailhub X-detected-operating-system: by eggs.gnu.org: GNU/Linux 3.x X-detected-operating-system: by eggs.gnu.org: Error: Malformed IPv6 address (bad octet value). X-Received-From: 2001:4830:134:3::11 X-Spam-Score: -1.6 (-) X-Debbugs-Envelope-To: submit X-Mailman-Approved-At: Thu, 29 Aug 2013 02:14:59 -0400 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.15 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.6 (-) --_000_E65DA92157873943BE52B62F964A934D0F30CAA7uqexmdb8soeuqed_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Dear Sir/Madam, I am writing this email to report a bug from od command. I am working in bi= oinformatics research filed, and currently I am trying to convert phred sco= res from fastq format file to Ascii values, and met weird things. For examp= le, when I try to convert 100 characters into ASCII values, if the last 30 = characters are the same, it only return part of values, NOT the complete va= lues. The example is listed below: If there is very long poly-# string, then below 100 characters only return = 84 ASCII values. $ echo '=3D:?D+AAB

Dear Sir/Madam,

 

I am writing this email to repo= rt a bug from od command. I am working in bioinformatics research filed, an= d currently I am trying to convert phred scores from fastq format file to A= scii values, and met weird things. For example, when I try to convert 100 characters into ASCII values, if the la= st 30 characters are the same, it only return part of values, NOT the compl= ete values.

The example is listed below:

If there is very long poly-# st= ring, then below 100 characters only return 84 ASCII values.

 

$ echo '=3D:?D+AAB<B?DCA= FEBAF?GHIBGFGCDGBGAFG8CF?F?D=3DDG?BFHG=3D@77C##############################= ###############' | od -An -t dC

   61   58&= nbsp;  63   68   43   65   65&= nbsp;  66   60   66   63   68&= nbsp;  67   65   70   69

   66   65&= nbsp;  70   63   71   72   73&= nbsp;  66   71   70   71   67&= nbsp;  68   71   66   71

   65   70&= nbsp;  71   56   67   70   63&= nbsp;  70   63   68   61   68&= nbsp;  71   63   66   70

   72   71&= nbsp;  61   64   55   55   67&= nbsp;  35   35   35   35   35&= nbsp;  35   35   35   35

   35   35&= nbsp;  35   35   35   35   35&= nbsp;  35   35   35   35   35&= nbsp;  35   35   35   35

*

   35   35&= nbsp;  35   35   10

 

If I changed the last poly-# wi= th one different character, it can return the full 100 ASCII values. Please= see below:

 

$ echo '=3D:?D+AAB<B?DCA= FEBAF?GHIBGFGCDGBGAFG8CF?F?D=3DDG?BFHG=3D@77C######################A#######= ###############' | od -An -t dC

   61   58&= nbsp;  63   68   43   65   65&= nbsp;  66   60   66   63   68&= nbsp;  67   65   70   69

   66   65&= nbsp;  70   63   71   72   73&= nbsp;  66   71   70   71   67&= nbsp;  68   71   66   71

   65   70&= nbsp;  71   56   67   70   63&= nbsp;  70   63   68   61   68&= nbsp;  71   63   66   70

   72   71&= nbsp;  61   64   55   55   67&= nbsp;  35   35   35   35   35&= nbsp;  35   35   35   35

   35   35&= nbsp;  35   35   35   35   35&= nbsp;  35   35   35   35   35&= nbsp;  35   65   35   35

   35   35&= nbsp;  35   35   35   35   35&= nbsp;  35   35   35   35   35&= nbsp;  35   35   35   35

   35   35&= nbsp;  35   35   10

 

Above command is running in Ubu= ntu environment. I am looking forward to your reply.

 

 

Cheers,

Kaitao Lai

--_000_E65DA92157873943BE52B62F964A934D0F30CAA7uqexmdb8soeuqed_-- From debbugs-submit-bounces@debbugs.gnu.org Thu Aug 29 07:51:29 2013 Received: (at control) by debbugs.gnu.org; 29 Aug 2013 11:51:29 +0000 Received: from localhost ([127.0.0.1]:35454 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.80) (envelope-from ) id 1VF0l3-00056m-Mo for submit@debbugs.gnu.org; Thu, 29 Aug 2013 07:51:29 -0400 Received: from mx1.redhat.com ([209.132.183.28]:24460) by debbugs.gnu.org with esmtp (Exim 4.80) (envelope-from ) id 1VF0ku-00056Q-Jc; Thu, 29 Aug 2013 07:51:20 -0400 Received: from int-mx09.intmail.prod.int.phx2.redhat.com (int-mx09.intmail.prod.int.phx2.redhat.com [10.5.11.22]) by mx1.redhat.com (8.14.4/8.14.4) with ESMTP id r7TBpFs5008968 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=OK); Thu, 29 Aug 2013 07:51:15 -0400 Received: from [10.3.113.179] (ovpn-113-179.phx2.redhat.com [10.3.113.179]) by int-mx09.intmail.prod.int.phx2.redhat.com (8.14.4/8.14.4) with ESMTP id r7TBpFZI013304; Thu, 29 Aug 2013 07:51:15 -0400 Message-ID: <521F35B2.9090608@redhat.com> Date: Thu, 29 Aug 2013 05:51:14 -0600 From: Eric Blake Organization: Red Hat, Inc. User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:17.0) Gecko/20130805 Thunderbird/17.0.8 MIME-Version: 1.0 To: Kaitao Lai Subject: Re: bug#15206: Report od bugs References: In-Reply-To: X-Enigmail-Version: 1.5.2 OpenPGP: url=http://people.redhat.com/eblake/eblake.gpg Content-Type: multipart/signed; micalg=pgp-sha256; protocol="application/pgp-signature"; boundary="PI5s8Ea1v0Wt4NMqMXGjXWh2qjFct4grE" X-Scanned-By: MIMEDefang 2.68 on 10.5.11.22 X-Spam-Score: -5.8 (-----) X-Debbugs-Envelope-To: control Cc: 15206-done@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.15 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -5.8 (-----) This is an OpenPGP/MIME signed message (RFC 4880 and 3156) --PI5s8Ea1v0Wt4NMqMXGjXWh2qjFct4grE Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable tag 15206 notabug thanks On 08/29/2013 12:01 AM, Kaitao Lai wrote: > Dear Sir/Madam, >=20 > I am writing this email to report a bug from od command. I am working i= n bioinformatics research filed, and currently I am trying to convert phr= ed scores from fastq format file to Ascii values, and met weird things. F= or example, when I try to convert 100 characters into ASCII values, if th= e last 30 characters are the same, it only return part of values, NOT the= complete values. > The example is listed below: > If there is very long poly-# string, then below 100 characters only ret= urn 84 ASCII values. >=20 > $ echo '=3D:?D+AAB 61 58 63 68 43 65 65 66 60 66 63 68 67 65 = 70 69 > 66 65 70 63 71 72 73 66 71 70 71 67 68 71 = 66 71 > 65 70 71 56 67 70 63 70 63 68 61 68 71 63 = 66 70 > 72 71 61 64 55 55 67 35 35 35 35 35 35 35 = 35 35 > 35 35 35 35 35 35 35 35 35 35 35 35 35 35 = 35 35 > * > 35 35 35 35 10 This behavior is documented, and required by POSIX. http://pubs.opengroup.org/onlinepubs/9699919799/utilities/od.html If you don't want elision of identical lines, then you must use the -v option. As this is working as intended, and is just usage error on your part, I'm marking this as not a bug. Feel free to add further comments or questions to this report, though. --=20 Eric Blake eblake redhat com +1-919-301-3266 Libvirt virtualization library http://libvirt.org --PI5s8Ea1v0Wt4NMqMXGjXWh2qjFct4grE Content-Type: application/pgp-signature; name="signature.asc" Content-Description: OpenPGP digital signature Content-Disposition: attachment; filename="signature.asc" -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.14 (GNU/Linux) Comment: Public key at http://people.redhat.com/eblake/eblake.gpg Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iQEcBAEBCAAGBQJSHzWyAAoJEKeha0olJ0Nq5aYH/1VwaOH75OhpxENgS54KvZSM C6N/Z9JOuu6qKRj/zPwSMzy4n3HIS3/QqTrtQyZk2TyCrpjN4pBdf+rXxb7rzjCl xSucq3atMgNF13J3YwUlsCSZxt/D8rsJR5gdeDfk6VKqHhTPIXpuMt73UXK1kPn+ eE3olzCuSoTnAL50f21CFCxi+zbluYbqExs+aEFE6Wy3iLPjxbtT03HxiaTMswvy IiEggu7HehYY4c5yOpLg8iVSQPLbRr2JdTBLFfkV8PaAOxHkbtUYqxbg5i35QESg twGVEIB0DjgTROAc2bwnQh+M0vnTOmlVPtPVm6eo4bIASOGJE4FeEiBfVPVc+O8= =Epn7 -----END PGP SIGNATURE----- --PI5s8Ea1v0Wt4NMqMXGjXWh2qjFct4grE-- From debbugs-submit-bounces@debbugs.gnu.org Thu Aug 29 08:28:34 2013 Received: (at 15206) by debbugs.gnu.org; 29 Aug 2013 12:28:34 +0000 Received: from localhost ([127.0.0.1]:35542 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.80) (envelope-from ) id 1VF1Kz-00071i-RK for submit@debbugs.gnu.org; Thu, 29 Aug 2013 08:28:34 -0400 Received: from mail3.vodafone.ie ([213.233.128.45]:57999) by debbugs.gnu.org with esmtp (Exim 4.80) (envelope-from ) id 1VF1Ky-00071Z-4S for 15206@debbugs.gnu.org; Thu, 29 Aug 2013 08:28:33 -0400 X-IronPort-Anti-Spam-Filtered: true X-IronPort-Anti-Spam-Result: ApQBALI9H1JtTGMW/2dsb2JhbAANTQ6DLkuDLb0BgUCDGAEBAQQjDwFWCw0LAgIFFgsCAgkDAgECAUUHDAgBAYgEBaVqdJIvgSmNAoFQgmiBNAOZIoUkjXRAgXA Received: from unknown (HELO [192.168.1.79]) ([109.76.99.22]) by mail3.vodafone.ie with ESMTP; 29 Aug 2013 13:28:30 +0100 Message-ID: <521F3E6D.6070202@draigBrady.com> Date: Thu, 29 Aug 2013 13:28:29 +0100 From: =?UTF-8?B?UMOhZHJhaWcgQnJhZHk=?= User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:17.0) Gecko/20130110 Thunderbird/17.0.2 MIME-Version: 1.0 To: 15206@debbugs.gnu.org, k.lai1@uq.edu.au Subject: Re: bug#15206: Report od bugs References: <521F35B2.9090608@redhat.com> In-Reply-To: <521F35B2.9090608@redhat.com> X-Enigmail-Version: 1.5.2 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Spam-Score: 1.7 (+) X-Spam-Report: Spam detection software, running on the system "debbugs.gnu.org", has identified this incoming email as possible spam. The original message has been attached to this so you can view it (if it isn't spam) or label similar future email. If you have any questions, see the administrator of that system for details. Content preview: On 08/29/2013 12:51 PM, Eric Blake wrote: > tag 15206 notabug > thanks > > On 08/29/2013 12:01 AM, Kaitao Lai wrote: >> Dear Sir/Madam, >> >> I am writing this email to report a bug from od command. I am working in bioinformatics research filed, and currently I am trying to convert phred scores from fastq format file to Ascii values, and met weird things. For example, when I try to convert 100 characters into ASCII values, if the last 30 characters are the same, it only return part of values, NOT the complete values. >> The example is listed below: >> If there is very long poly-# string, then below 100 characters only return 84 ASCII values. >> >> $ echo '=:?D+AAB> 61 58 63 68 43 65 65 66 60 66 63 68 67 65 70 69 >> 66 65 70 63 71 72 73 66 71 70 71 67 68 71 66 71 >> 65 70 71 56 67 70 63 70 63 68 61 68 71 63 66 70 >> 72 71 61 64 55 55 67 35 35 35 35 35 35 35 35 35 >> 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 >> * >> 35 35 35 35 10 > > This behavior is documented, and required by POSIX. > http://pubs.opengroup.org/onlinepubs/9699919799/utilities/od.html > > If you don't want elision of identical lines, then you must use the -v > option. > > As this is working as intended, and is just usage error on your part, > I'm marking this as not a bug. Feel free to add further comments or > questions to this report, though. > [...] Content analysis details: (1.7 points, 10.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- -0.0 RCVD_IN_DNSWL_NONE RBL: Sender listed at http://www.dnswl.org/, no trust [213.233.128.45 listed in list.dnswl.org] 1.7 DEAR_SOMETHING BODY: Contains 'Dear (something)' X-Debbugs-Envelope-To: 15206 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.15 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.7 (+) X-Spam-Report: Spam detection software, running on the system "debbugs.gnu.org", has identified this incoming email as possible spam. The original message has been attached to this so you can view it (if it isn't spam) or label similar future email. If you have any questions, see the administrator of that system for details. Content preview: On 08/29/2013 12:51 PM, Eric Blake wrote: > tag 15206 notabug > thanks > > On 08/29/2013 12:01 AM, Kaitao Lai wrote: >> Dear Sir/Madam, >> >> I am writing this email to report a bug from od command. I am working in bioinformatics research filed, and currently I am trying to convert phred scores from fastq format file to Ascii values, and met weird things. For example, when I try to convert 100 characters into ASCII values, if the last 30 characters are the same, it only return part of values, NOT the complete values. >> The example is listed below: >> If there is very long poly-# string, then below 100 characters only return 84 ASCII values. >> >> $ echo '=:?D+AAB> 61 58 63 68 43 65 65 66 60 66 63 68 67 65 70 69 >> 66 65 70 63 71 72 73 66 71 70 71 67 68 71 66 71 >> 65 70 71 56 67 70 63 70 63 68 61 68 71 63 66 70 >> 72 71 61 64 55 55 67 35 35 35 35 35 35 35 35 35 >> 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 >> * >> 35 35 35 35 10 > > This behavior is documented, and required by POSIX. > http://pubs.opengroup.org/onlinepubs/9699919799/utilities/od.html > > If you don't want elision of identical lines, then you must use the -v > option. > > As this is working as intended, and is just usage error on your part, > I'm marking this as not a bug. Feel free to add further comments or > questions to this report, though. > [...] Content analysis details: (1.7 points, 10.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- -0.0 RCVD_IN_DNSWL_NONE RBL: Sender listed at http://www.dnswl.org/, no trust [213.233.128.45 listed in list.dnswl.org] 1.7 DEAR_SOMETHING BODY: Contains 'Dear (something)' On 08/29/2013 12:51 PM, Eric Blake wrote: > tag 15206 notabug > thanks > > On 08/29/2013 12:01 AM, Kaitao Lai wrote: >> Dear Sir/Madam, >> >> I am writing this email to report a bug from od command. I am working in bioinformatics research filed, and currently I am trying to convert phred scores from fastq format file to Ascii values, and met weird things. For example, when I try to convert 100 characters into ASCII values, if the last 30 characters are the same, it only return part of values, NOT the complete values. >> The example is listed below: >> If there is very long poly-# string, then below 100 characters only return 84 ASCII values. >> >> $ echo '=:?D+AAB> 61 58 63 68 43 65 65 66 60 66 63 68 67 65 70 69 >> 66 65 70 63 71 72 73 66 71 70 71 67 68 71 66 71 >> 65 70 71 56 67 70 63 70 63 68 61 68 71 63 66 70 >> 72 71 61 64 55 55 67 35 35 35 35 35 35 35 35 35 >> 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 >> * >> 35 35 35 35 10 > > This behavior is documented, and required by POSIX. > http://pubs.opengroup.org/onlinepubs/9699919799/utilities/od.html > > If you don't want elision of identical lines, then you must use the -v > option. > > As this is working as intended, and is just usage error on your part, > I'm marking this as not a bug. Feel free to add further comments or > questions to this report, though. > Also in case it's of any use, there was mention of fastq processing in: http://bugs.gnu.org/13089#15 cheers, Pádraig. From unknown Sun Aug 17 09:10:32 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Fri, 27 Sep 2013 11:24:03 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator