Refresh existing patches

diff --git a/debian/patches/adding-include-hts-dirs b/debian/patches/adding-include-hts-dirs
index 129fa828e4adc8a0b7a9526562f2379dd7c22ed7..5f3194c220a38c2889f2d005e002952870b504f1 100644 (file)
--- a/debian/patches/adding-include-hts-dirs
+++ b/debian/patches/adding-include-hts-dirs
@@ -1,7 +1,7 @@
 Description: Added the include dirs
 --- python-pysam.orig/setup.py
 +++ python-pysam/setup.py
-@@ -103,6 +103,7 @@
+@@ -116,6 +116,7 @@
      chtslib_sources = []
      shared_htslib_sources = htslib_sources
      htslib_library_dirs = HTSLIB_LIBRARY_DIR

diff --git a/debian/patches/change-htslib-statement-to-link-to-debian b/debian/patches/change-htslib-statement-to-link-to-debian
index 045e3027cff7aaf0be4fe5a638a7e1dcd7a8c47e..d607a0f2175a0c2f809079f300ab81b41f83050a 100644 (file)
--- a/debian/patches/change-htslib-statement-to-link-to-debian
+++ b/debian/patches/change-htslib-statement-to-link-to-debian
@@ -1,7 +1,7 @@
 Description: Trying to bind to debian htslib
 --- python-pysam.orig/setup.py
 +++ python-pysam/setup.py
-@@ -30,7 +30,7 @@
+@@ -43,7 +43,7 @@
  #         pysam.
  # external: use shared libhts.so compiled outside of
  #           pysam
@@ -10,7 +10,7 @@ Description: Trying to bind to debian htslib
  HTSLIB_LIBRARY_DIR = os.environ.get('HTSLIB_LIBRARY_DIR', None)
  HTSLIB_INCLUDE_DIR = os.environ.get('HTSLIB_INCLUDE_DIR', None)
  
-@@ -98,6 +98,12 @@
+@@ -111,6 +111,12 @@
      htslib_library_dirs = ['pysam']
      htslib_include_dirs = ['htslib']
      htslib_libraries = ['chtslib']

diff --git a/debian/patches/ignore-htslib-dir.patch b/debian/patches/ignore-htslib-dir.patch
index 0a733439a4a602f6c16f6d2c489e6392e72bc958..2ca4cd7e626de3c5ca1e334922c175f2767f3ad2 100644 (file)
--- a/debian/patches/ignore-htslib-dir.patch
+++ b/debian/patches/ignore-htslib-dir.patch
@@ -8,7 +8,7 @@ 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
-@@ -476,8 +476,6 @@
+@@ -490,8 +490,6 @@
      'url': "https://github.com/pysam-developers/pysam",
      'packages': ['pysam',
                   'pysam.include',
@@ -17,8 +17,8 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
                   'pysam.include.samtools',
                   # 'pysam.include.samtools.bcftools',
                   'pysam.include.samtools.win32'],
-@@ -493,7 +493,6 @@
-                     faidx],
+@@ -509,7 +507,6 @@
+                     cutils],
      'cmdclass': cmdclass,
      'package_dir': {'pysam': 'pysam',
 -                    'pysam.include.htslib': 'htslib',