This patch modifies the build process such that the bundled copy of pysam does
not need to be built if CROSSMAP_USE_SYSTEM_PYSAM is set and the pysam module
can be imported.

Upstream has agreed to apply the patch in the next maintenance release of
crossmap.  The patch has already been uploaded to
http://sourceforge.net/projects/crossmap/files/patch/.

diff --git a/setup.py b/setup.py
--- a/setup.py	2015-02-26 15:28:49.771189185 +0100
+++ b/setup.py	2015-02-26 15:55:03.440327752 +0100
@@ -19,6 +19,15 @@
 except:
 	have_numpy = False
 
+try:
+	import pysam
+	if os.environ['CROSSMAP_USE_SYSTEM_PYSAM']:
+		have_pysam = True
+	else:
+		have_pysam = False
+except ImportError:
+	have_pysam = False
+
 if platform.system()=='Windows':
 	print >> sys.stderr, "Sorry, Windows platform is not supported!"
 	sys.exit()
@@ -165,49 +174,50 @@
 	
 	
 	#================= pysam samtools ====================
-	extensions.append(Extension(
-    	"pysam.csamtools",              
-		csamtools_sources + [ "lib/pysam/%s" % x for x in ("pysam_util.c", )] +\
-		glob.glob( os.path.join( "lib/samtools", "*.pysam.c" )) +\
-		os_c_files + \
-		glob.glob( os.path.join( "lib/samtools", "*", "*.pysam.c" ) ),
-		library_dirs=[],
-		include_dirs=[ "lib/samtools", "lib/pysam" ] + include_os,
-		libraries=[ "z", ],
-		language="c",
-		define_macros = [('_FILE_OFFSET_BITS','64'),('_USE_KNETFILE','')], 
-    ))
-
-	extensions.append(Extension(
-		"pysam.ctabix",                   
-		tabix_sources + [ "lib/pysam/%s" % x for x in ( "tabix_util.c", )] +\
-		os_c_files + \
-		glob.glob( os.path.join( "lib/tabix", "*.pysam.c" ) ),
-		library_dirs=[],
-		include_dirs=[ "lib/tabix", "lib/pysam" ] + include_os,
-		libraries=[ "z", ],
-		language="c",
-		define_macros = [('_FILE_OFFSET_BITS','64'),
-                     ('_USE_KNETFILE','')], 
-    ))
-
-	extensions.append(Extension(
-		"pysam.TabProxies",               
-		tabproxies_sources + os_c_files,
-		library_dirs=[],
-		include_dirs= include_os,
-		libraries=[ "z", ],
-		language="c",
-    ))
-
-	extensions.append(Extension(
-		"pysam.cvcf",                   
-		cvcf_sources + os_c_files,
-		library_dirs=[],
-		include_dirs= ["lib/tabix",] + include_os,
-		libraries=[ "z", ],
-		language="c",
-    ))
+        if not have_pysam:
+                extensions.append(Extension(
+                        "pysam.csamtools",              
+                        csamtools_sources + [ "lib/pysam/%s" % x for x in ("pysam_util.c", )] +\
+                        glob.glob( os.path.join( "lib/samtools", "*.pysam.c" )) +\
+                        os_c_files + \
+                        glob.glob( os.path.join( "lib/samtools", "*", "*.pysam.c" ) ),
+                        library_dirs=[],
+                        include_dirs=[ "lib/samtools", "lib/pysam" ] + include_os,
+                        libraries=[ "z", ],
+                        language="c",
+                        define_macros = [('_FILE_OFFSET_BITS','64'),('_USE_KNETFILE','')], 
+                ))
+
+                extensions.append(Extension(
+                        "pysam.ctabix",                   
+                        tabix_sources + [ "lib/pysam/%s" % x for x in ( "tabix_util.c", )] +\
+                        os_c_files + \
+                        glob.glob( os.path.join( "lib/tabix", "*.pysam.c" ) ),
+                        library_dirs=[],
+                        include_dirs=[ "lib/tabix", "lib/pysam" ] + include_os,
+                        libraries=[ "z", ],
+                        language="c",
+                        define_macros = [('_FILE_OFFSET_BITS','64'),
+                                         ('_USE_KNETFILE','')], 
+                ))
+
+                extensions.append(Extension(
+                        "pysam.TabProxies",               
+                        tabproxies_sources + os_c_files,
+                        library_dirs=[],
+                        include_dirs= include_os,
+                        libraries=[ "z", ],
+                        language="c",
+                ))
+
+                extensions.append(Extension(
+                        "pysam.cvcf",                   
+                        cvcf_sources + os_c_files,
+                        library_dirs=[],
+                        include_dirs= ["lib/tabix",] + include_os,
+                        libraries=[ "z", ],
+                        language="c",
+                ))
 
 
 	return extensions     
itle='2021-04-27 13:57:45 +0200'>2021-04-27</span></td><td><a href='/guix/commit/gnu/packages/textutils.scm?id=5c81cbda5e1c97b5234f48f36de28adcccaa3555'>gnu: html2text: Fix cross-compilation.</a><span class='msg-avail'>...<span class='msg-tooltip'>* gnu/packages/textutils.scm (html2text)[arguments]: Set $CXX to
the correct (CC-FOR-TARGET).
</span></span></td><td>Tobias Geerinckx-Rice</td></tr>
<tr><td><span title='2021-04-27 13:54:44 +0200'>2021-04-27</span></td><td><a href='/guix/commit/gnu/packages/textutils.scm?id=b0020938e17ac4d7f9f87d9bb7ff2d2dbdd7c33f'>gnu: html2text: Run ./configure without errors.</a><span class='msg-avail'>...<span class='msg-tooltip'>* gnu/packages/textutils.scm (html2text)[arguments]: Add a custom
'configure phase.  Replace the custom 'fix-paths phase with the
customary #:make-flags equivalent.
</span></span></td><td>Tobias Geerinckx-Rice</td></tr>
<tr><td><span title='2021-04-27 13:36:16 +0200'>2021-04-27</span></td><td><a href='/guix/commit/gnu/packages/textutils.scm?id=b43e9c8ecd44b597936033eb441f50980d00c398'>gnu: Add html2text.</a><span class='msg-avail'>...<span class='msg-tooltip'>* gnu/packages/textutils.scm (html2text): New variable.
</span></span></td><td>Guillaume Le Vaillant</td></tr>
<tr><td><span title='2021-03-13 14:26:02 +0100'>2021-03-13</span></td><td><a href='/guix/commit/gnu/packages/textutils.scm?id=2ee7524c76e32e5277af40b4b55aa3ac4e421f19'>gnu: opencc: Update to 1.1.1.</a><span class='msg-avail'>...<span class='msg-tooltip'>* gnu/packages/textutils.scm(opencc): Update to 1.1.1
[arguments]&lt;#:out-of-source?&gt;: Build in source tree.
&lt;#:parallel-build?&gt;: Disable.
&lt;#:phases&gt;: In "patch-3rd-party-references", fix the version of dependency.
Add phases "patch-python-binding-installation", "install-python-binding"
and "enable-bytecode-determinism".
[native-inputs]: Add python-setuptools and python-wheel.

Signed-off-by: Nicolas Goaziou &lt;mail@nicolasgoaziou.fr&gt;
</span></span></td><td>Zhu Zihao</td></tr>