Hello,
I had built our own version of samtools so it created a shared library. It then ocurred to me to try building pysam against this shared library. I was able make it work well enough to run pysams test cases.
Would modifying the debian samtools and tabix packages to build shared objects be a reasonable solution to the pysam code copying problem?
Methods:
I only tried changing pysam to link to my samtools shared library, I didn't bother trying to fix the wholesale import of tabix. (I was curious if the shared object strategy would work).
To make it work I needed add the following object files to the libbam so.
bam_plcmd.o sam_view.o
bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o
bam2bcf.o bam2bcf_indel.o errmod.o sample.o
cut_target.o phase.o bam2depth.o
bcftools/bcf.o bcftools/bcfutils.o bcftools/fet.o
quilt patch file:
http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blob;f=debian/patches/phase-in-so;h=64f44beebe4120c2c2c6ae792442a75d5bb256b3;hb=woldlab
On the pysam side I told it to use my include/bam and library and
pulled out the wholesale importing of samptools/*.pysam.c
It ran well enough to run the tests, though there may still be some undefined symbols, as I didn't add all the *.o's that the pysam setup.py was using.
--- setup.orig.py 2012-12-19 12:27:21.019867664 -0800
+++ setup.py 2012-12-19 15:20:29.191500964 -0800
@@ -138,22 +138,20 @@
if platform.system()=='Windows':
include_os = ['win32']
os_c_files = ['win32/getopt.c']
else:
- include_os = []
+ include_os = ['/usr/include/bam']
os_c_files = []
samtools = Extension(
"csamtools", # name of extension
[ "pysam/csamtools.pyx" ] +\
[ "pysam/%s" % x for x in (
"pysam_util.c", )] +\
- glob.glob( os.path.join( "samtools", "*.pysam.c" )) +\
- os_c_files + \
- glob.glob( os.path.join( "samtools", "*", "*.pysam.c" ) ),
+ os_c_files ,
library_dirs=[],
- include_dirs=[ "samtools", "pysam" ] + include_os,
- libraries=[ "z", ],
+ include_dirs=["pysam" ] + include_os,
+ libraries=[ "z", "bam"],
language="c",
Diane
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