Hi, The other pysam dependency is tabix which I tried to convert it to a shared library.
I put my patch to make tabix use libtool to build static, linux or os x shared libraries at [1]: However I haven't modified the debian package to actually build a libtabix1 and libtabix-dev package. I discovered that tabix & samtools include slightly different versions of klib[2]. It looks like klib doesn't believe in don't-repeat-yourself as they don't provide a makefile and their readme encourages people to just copy klib files into their own software. Since pysam includes both of samtools and tabix it ends up with duplicates of files: bgzf.[ch], knetfile.[ch], kseq.h, ksort.h, and kstring.[ch] A quick diff between the pysam samtools and tabix directories shows bgzf.c has a different api. I'd like to avoid cleaning up the klib mess, would it be reasonable to have the header files for samtools in something like "/usr/include/bam" and tabix as "/usr/include/tabix"? Also just to check, can does the dynamic linker treat the same symbol name in two different shared libraries as different? Diane [1] http://woldlab.caltech.edu/gitweb/?p=tabix.git;a=blob;f=debian/patches/use-libtool;h=58cde517e8e4c6a1c48c5c188399642abe726b7f;hb=build-so [2] https://github.com/attractivechaos/klib
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