From bcff0a2b53414b4b17a713044d5b910db76cda44 Mon Sep 17 00:00:00 2001
From: Afif Elghraoui <afif@ghraoui.name>
Date: Sat, 5 Mar 2016 16:36:03 -0800
Subject: [PATCH] Update patch for external HTSlib

---
 debian/patches/external-htslib.patch   | 84 ++++++++++++++++++++++++++
 debian/patches/ignore-htslib-dir.patch | 27 ---------
 debian/patches/series                  |  2 +-
 3 files changed, 85 insertions(+), 28 deletions(-)
 create mode 100644 debian/patches/external-htslib.patch
 delete mode 100644 debian/patches/ignore-htslib-dir.patch

diff --git a/debian/patches/external-htslib.patch b/debian/patches/external-htslib.patch
new file mode 100644
index 0000000..9160eb8
--- /dev/null
+++ b/debian/patches/external-htslib.patch
@@ -0,0 +1,84 @@
+Description: Fix external htslib support
+Author: Afif Elghraoui <afif@debian.org>
+Forwarded: no
+Last-Update: 2016-03-05
+--- python-pysam.orig/setup.py
++++ python-pysam/setup.py
+@@ -87,10 +87,20 @@
+ #         pysam.
+ # external: use shared libhts.so compiled outside of
+ #           pysam
+-HTSLIB_MODE = "shared"
++HTSLIB_MODE = os.environ.get("HTSLIB_MODE","shared")
+ HTSLIB_LIBRARY_DIR = os.environ.get("HTSLIB_LIBRARY_DIR", None)
+ HTSLIB_INCLUDE_DIR = os.environ.get("HTSLIB_INCLUDE_DIR", None)
+ HTSLIB_CONFIGURE_OPTIONS = os.environ.get("HTSLIB_CONFIGURE_OPTIONS", None)
++HTSLIB_SOURCE = None
++
++package_list = ['pysam',
++                'pysam.include',
++                'pysam.include.samtools',
++                'pysam.include.bcftools',
++                'pysam.include.samtools.win32']
++package_dirs = {'pysam': 'pysam',
++                'pysam.include.samtools': 'samtools',
++                'pysam.include.bcftools': 'bcftools'}
+ 
+ # Check if cython is available
+ #
+@@ -101,13 +111,15 @@
+     from cy_build import CyExtension as Extension, cy_build_ext as build_ext
+     source_pattern = "pysam/c%s.pyx"
+     cmdclass = {'build_ext': build_ext}
+-    HTSLIB_MODE = "shared"
++    if HTSLIB_MODE != "external":
++        HTSLIB_MODE = "shared"
+ except ImportError:
+     # no Cython available - use existing C code
+     cmdclass = {}
+     source_pattern = "pysam/c%s.c"
+     # Set mode to separate, as "shared" not fully tested yet.
+-    HTSLIB_MODE = "separate"
++    if HTSLIB_MODE != "external":
++        HTSLIB_MODE = "separate"
+ 
+ # collect pysam version
+ sys.path.insert(0, "pysam")
+@@ -140,6 +152,10 @@
+ htslib_configure_options = None
+ 
+ if HTSLIB_MODE in ['shared', 'separate']:
++    package_list += ['pysam.include.htslib',
++                     'pysam.include.htslib.htslib']
++    package_dirs.update({'pysam.include.htslib':'htslib'})
++
+     htslib_configure_options = configure_library(
+         "htslib",
+         HTSLIB_CONFIGURE_OPTIONS,
+@@ -492,13 +508,7 @@
+     'license': "MIT",
+     'platforms': "ALL",
+     'url': "https://github.com/pysam-developers/pysam",
+-    'packages': ['pysam',
+-                 'pysam.include',
+-                 'pysam.include.htslib',
+-                 'pysam.include.htslib.htslib',
+-                 'pysam.include.samtools',
+-                 'pysam.include.bcftools',
+-                 'pysam.include.samtools.win32'],
++    'packages': package_list,
+     'requires': ['cython (>=0.21)'],
+     'ext_modules': [chtslib,
+                     csamfile,
+@@ -511,10 +521,7 @@
+                     cfaidx,
+                     cutils],
+     'cmdclass': cmdclass,
+-    'package_dir': {'pysam': 'pysam',
+-                    'pysam.include.htslib': 'htslib',
+-                    'pysam.include.samtools': 'samtools',
+-                    'pysam.include.bcftools': 'bcftools'},
++    'package_dir': package_dirs,
+     'package_data': {'': ['*.pxd', '*.h'], },
+     # do not pack in order to permit linking to csamtools.so
+     'zip_safe': False,
diff --git a/debian/patches/ignore-htslib-dir.patch b/debian/patches/ignore-htslib-dir.patch
deleted file mode 100644
index 395ff4f..0000000
--- a/debian/patches/ignore-htslib-dir.patch
+++ /dev/null
@@ -1,27 +0,0 @@
-Description: Allow setup.py to cope with missing htslib copy
- The build system expects the convenience copy to be present.
- This change allows the build to work without it. After all,
- we're linking with the Debian htslib package.
-Author: Afif Elghraoui
-Last-Update: 2015-06-24
----
-This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
---- python-pysam.orig/setup.py
-+++ python-pysam/setup.py
-@@ -494,8 +494,6 @@
-     'url': "https://github.com/pysam-developers/pysam",
-     'packages': ['pysam',
-                  'pysam.include',
--                 'pysam.include.htslib',
--                 'pysam.include.htslib.htslib',
-                  'pysam.include.samtools',
-                  'pysam.include.bcftools',
-                  'pysam.include.samtools.win32'],
-@@ -512,7 +510,6 @@
-                     cutils],
-     'cmdclass': cmdclass,
-     'package_dir': {'pysam': 'pysam',
--                    'pysam.include.htslib': 'htslib',
-                     'pysam.include.samtools': 'samtools',
-                     'pysam.include.bcftools': 'bcftools'},
-     'package_data': {'': ['*.pxd', '*.h'], },
diff --git a/debian/patches/series b/debian/patches/series
index 878b584..2417565 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,2 @@
-ignore-htslib-dir.patch
+external-htslib.patch
 disable-tests-requiring-network.patch
-- 
2.30.2