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, Heng 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 I also noticed that you are using an outdated copy of zlib and I have no 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 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". Trouble? Contact [email protected] Archive: http://lists.debian.org/[email protected]
