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Re: Usage of zlib in MaqView

Hello Andreas,

Thanks for your advice. Actually the preferred way is to use the more advanced technology developed for the BAM format. Nonetheless, it is a little too late.

As to *.java and *.pm, they are experimental and you can ignore them. You can only package maqview and its manual page.

Best wishes,


On Nov 23, 2010, at 11:44 AM, Andreas Tille wrote:

> Hello Heng,
> thanks for your clarification.
> On Tue, Nov 23, 2010 at 10:20:46AM -0500, Heng Li wrote:
>> Many thanks for considering to port maqview to Debian Med. Unfortunately, I am afraid that for maqview we have to include those private zlib headers because maqview must use very low-level zlib structs and functions in order to achieve random access in a generic gzip file.
> I have seen that you are using low level functions and I simply trust
> your word that this is the only way because I have no time for a deeper
> inspection.  However, if I were you I would probably consider poking
> zlib authors for an implementation of your requirement in a stable API.
> I also noticed that you are using an outdated copy of zlib and I have no
> idea about the security implications this might have.  So I'd suggest in
> any case to restructure your source code and put foreign code in a
> separate directory with a clean documentation what version is used and
> why.
>> At the same time, although maqview still has a few features that even the most modern viewers are missing, it is not the best any more (for example, IGV, which has been ported to Debian Med, is more generic and better).
> I've got another hint to IGV and I just tried it yesterday.  Thanks for
> the hint in any case.
>> If you have difficulty in porting maqview, you may consider not to include maqview in Debian Med. This would be unfortunate for us, but we are unable to drop the dependency. I am sorry.
> It is not actually *difficult* to build MaqView for Debian - it is just
> considered "dirty" to include copies of any library.  So before I'm
> doing dirty things I'm just checking whether there is a better way to
> do.
> Once we are at it, I have some other questions:
>  1. There is a MaqDataClient.java which builds two *.class files.
>     Can you please explain the role of this.  I have the impression
>     that these files are not really used.  Am I missing something?
>  2. I also failed to find some documentation about MaqIndex.pm and
>     maqindex_socket.pl and so I just installed the binaries which
>     are compiled from the C sources.  Any hint about the use of
>     these files?
> Kind regards and thanks for your comments
>      Andreas.
> -- 
> http://fam-tille.de

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