GNU bug report logs -
#15206
Report od bugs
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Reported by: Kaitao Lai <k.lai1 <at> uq.edu.au>
Date: Thu, 29 Aug 2013 06:16:02 UTC
Severity: normal
Tags: notabug
Done: Eric Blake <eblake <at> redhat.com>
Bug is archived. No further changes may be made.
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Your message dated Thu, 29 Aug 2013 05:51:14 -0600
with message-id <521F35B2.9090608 <at> redhat.com>
and subject line Re: bug#15206: Report od bugs
has caused the debbugs.gnu.org bug report #15206,
regarding Report od bugs
to be marked as done.
(If you believe you have received this mail in error, please contact
help-debbugs <at> gnu.org.)
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15206: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=15206
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Contact help-debbugs <at> gnu.org with problems
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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<B?DCAFEBAF?GHIBGFGCDGBGAFG8CF?F?D=DG?BFHG=@77C#############################################' | od -An -t dC
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
If I changed the last poly-# with one different character, it can return the full 100 ASCII values. Please see below:
$ echo '=:?D+AAB<B?DCAFEBAF?GHIBGFGCDGBGAFG8CF?F?D=DG?BFHG=@77C######################A######################' | od -An -t dC
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 65 35 35
35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35
35 35 35 35 10
Above command is running in Ubuntu environment. I am looking forward to your reply.
Cheers,
Kaitao Lai
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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<B?DCAFEBAF?GHIBGFGCDGBGAFG8CF?F?D=DG?BFHG=@77C#############################################' | od -An -t dC
> 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.
--
Eric Blake eblake redhat com +1-919-301-3266
Libvirt virtualization library http://libvirt.org
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This bug report was last modified 11 years and 328 days ago.
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