[Debian-med-packaging] Subject: libbam-dev: additional header files for package

[Alex Mestiashvili]

On 05/04/2011 06:19 PM, Charles Plessy wrote:
> Hi Alex,
>
> I got a similar request in Ubuntu.
>
> https://bugs.launchpad.net/ubuntu/+source/samtools/+bug/690997
>
> cufflinks and Bio::Samtools expect the libbam headers in different directories.
> It was briefly discussed upstream, but remained inconclusive.
>
> http://sourceforge.net/mailarchive/forum.php?thread_name=20110104103405.GB28632%40sanger.ac.uk&forum_name=samtools-devel
>
> We need to restart the discussion, or take action downstream.
>
> Cheers,
>
>    

Hello ,

I think that the placement of header files isn't very important ,
for example for cufflinks I just prepared 2 tiny patches which solve the 
problem when using /usr/include .
http://git.debian.org/?p=debian-med/cufflinks.git;a=tree;f=debian/patches;h=d97f5bbc0dfb9c2d5a659f21a38b5e389d5d3c93;hb=18588967fb57512852df763a2b44f923aa85e5d2

The only problem I see is that sam.h , bam.h ...  have very short and 
generic names .

for example:  there are already packages with such headers :

libadplug-dev: /usr/include/adplug/bam.h
libcorosync-dev: /usr/include/corosync/sam.h

So I think it is better to have samtools headers in a separate directory .

Another problem is that cufflinks needs additional header file
from samtools source - sam.h which isn't provided by libbam-dev .

I tried to build Bio::Samtools having headers in /usr/include/bam
and it is needed to fix just 2 files -Build.pl and Sam.xs to build it  
successfully .

Best regards ,

Alex