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

[Andreas Prlic]

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
>
>
>
>
>
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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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>
-----------------------------------------------------------------------

Andreas Prlic      Wellcome Trust Sanger Institute
                               Hinxton, Cambridge CB10 1SA, UK
			 +44 (0) 1223 49 6891