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

[Richard Holland]

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I have no idea what it is for. There are generic Java classes provided
with the SDK that do the same job. I think we should probably drop it.
Lets wait to see if anyone shouts first.

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
> 
> 
> 
> 
> 
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> 
> [ 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 ]
> 
> 
> _______________________________________________
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> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> 
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