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bug#15206: Report od bugs
From: |
Pádraig Brady |
Subject: |
bug#15206: Report od bugs |
Date: |
Thu, 29 Aug 2013 13:28:29 +0100 |
User-agent: |
Mozilla/5.0 (X11; Linux x86_64; rv:17.0) Gecko/20130110 Thunderbird/17.0.2 |
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<address@hidden' | 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.
>
Also in case it's of any use, there was mention of fastq processing in:
http://bugs.gnu.org/13089#15
cheers,
Pádraig.