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

[mark.schreiber at novartis.com]

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 ]