[med-svn] [python-pysam] 07/10: Refresh existing patches

[Afif Elghraoui]

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afif-guest pushed a commit to branch master
in repository python-pysam.

commit 21aac6cb038456176c781b6ed74372c3820fd26f
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Wed Nov 11 23:21:05 2015 -0800

    Refresh existing patches
---
 debian/patches/adding-include-hts-dirs                   | 2 +-
 debian/patches/change-htslib-statement-to-link-to-debian | 4 ++--
 debian/patches/ignore-htslib-dir.patch                   | 6 +++---
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/debian/patches/adding-include-hts-dirs b/debian/patches/adding-include-hts-dirs
index 129fa82..5f3194c 100644
--- 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 045e302..d607a0f 100644
--- 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 0a73343..2ca4cd7 100644
--- 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',

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