[Biojava-dev] Fwd: Bug in org/biojava/utils/io/UncompressInputStream.java

[Richard Holland]

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Andreas - did you write the class? If so, then you may understand it
better than the rest of us. Would you be willing to attempt to fix it?

cheers,
Richard

Andreas Prlic wrote:
> Hi!
> 
> I committed this class a while ago, since I did not find any other way 
> to read .Z compressed files.
> 
> Unfortunately PDB files are often stored like that  ...
> 
> If anybody has a suggestion how to read unix compressed files (.Z) in a 
> better way, I would be glad to hear.
> 
> Parsing them as Zip or GZip did not work in my trials...
> 
> Andreas
> 
> 
> 
> 
> 
> On 9 Apr 2007, at 03:13, mark.schreiber at novartis.com wrote:
> 
>> Does anyone maintain this class??
>>
>> More to the point, does anyone know what it is for??? If I look at the
>> Uses link in javadoc there are aparently none at the public or package
>> level. Additionally why does biojava need one, are there not java.io
>> classes that can handle compressed streams??
>>
>> Is there a good reason why we cannot just clean it out?
>>
>> - Mark
>>
>> Mark Schreiber
>> Research Investigator (Bioinformatics)
>>
>> Novartis Institute for Tropical Diseases (NITD)
>> 10 Biopolis Road
>> #05-01 Chromos
>> Singapore 138670
>> www.nitd.novartis.com
>>
>> phone +65 6722 2973
>> fax  +65 6722 2910
>>
>>
>>
>>
>>
>> Chris Dagdigian <dag at sonsorol.org>
>> Sent by: biojava-dev-bounces at lists.open-bio.org
>> 04/07/2007 09:52 AM
>>
>>
>>         To:     biojava-dev at biojava.org
>>         cc:     (bcc: Mark Schreiber/GP/Novartis)
>>         Subject:        [Biojava-dev] Fwd: Bug in 
>> org/biojava/utils/io/UncompressInputStream.java
>>
>>
>>
>> Passing on this email that came to me ...
>>
>> Regards,
>> Chris Dagdigian
>> OBF
>>
>>
>> Begin forwarded message:
>>
>>> From: "Miguel Duarte" <malduarte at gmail.com>
>>> Date: April 6, 2007 2:16:52 PM EDT
>>> To: dag at sonsorol.org
>>> Subject: Bug in org/biojava/utils/io/UncompressInputStream.java
>>>
>>> Hi Chris,
>>>
>>>> From http://sourceforge.net/project/shownotes.php?
>>>> release_id=314770&group_id=18598,
>>> i've learned that you're maintaining the class
>>> org/biojava/utils/io/UncompressInputStream.java. If that's not the
>>> case please forward this mail to the maintainer.
>>>
>>> I've discovered a nasty bug: With some read block sizes the algorithm
>>> truncates a few bytes from the end of the stream. I've verified this
>>> comparing the gzip/uncompress output for some files versus what
>>> org/biojava/utils/io/UncompressInputStream.java generates.
>>>
>>> Unfortunately i've not discovered the bug yet, but i can contribute
>>> with the attached test case. How to verify the bug:
>>> uncompress BH_03834.MCR.Z with gzip and with UncompressInputStream and
>>> compare the results.
>>>
>>> Thanks,
>>> Miguel Duarte
>>
>>
>>
>>
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
>> [ Attachment ''BH_03834.MCR.Z'' removed by Mark Schreiber ]
>> [ Attachment ''UNCOMPRESSED_BY_GZIP'' removed by Mark Schreiber ]
>> [ Attachment ''UNCOMPRESSED_BY_UNCOMPRESSINPUTSTREAM'' removed by Mark
>> Schreiber ]
>>
>>
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
>>
> -----------------------------------------------------------------------
> 
> Andreas Prlic      Wellcome Trust Sanger Institute
>                                Hinxton, Cambridge CB10 1SA, UK
> 			 +44 (0) 1223 49 6891
> 
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> 
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