[med-svn] [python-pysam] 05/07: Support building with missing htslib directory

[Afif Elghraoui]

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

commit bb5c719166e7c3a79a68b4821f9f74a0104fbb0a
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Wed Jun 24 21:14:23 2015 -0700

    Support building with missing htslib directory
---
 debian/changelog                             |  2 +-
 debian/patches/correct-spelling-errors.patch | 11 -----------
 debian/patches/ignore-htslib-dir.patch       | 27 +++++++++++++++++++++++++++
 debian/patches/series                        |  1 +
 4 files changed, 29 insertions(+), 12 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 5cde36a..3cbc0c5 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-python-pysam (0.8.3-1) UNRELEASED; urgency=medium
+python-pysam (0.8.3+ds1-1) UNRELEASED; urgency=medium
 
   * Team upload.
 
diff --git a/debian/patches/correct-spelling-errors.patch b/debian/patches/correct-spelling-errors.patch
index 84e5644..0b9c5cb 100644
--- a/debian/patches/correct-spelling-errors.patch
+++ b/debian/patches/correct-spelling-errors.patch
@@ -4,17 +4,6 @@ Bug: https://github.com/pysam-developers/pysam/pull/122
 Last-Update: 2015-06-09
 ---
 This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
---- python-pysam.orig/htslib/cram/cram_index.c
-+++ python-pysam/htslib/cram/cram_index.c
-@@ -315,7 +315,7 @@
- 
- /*
-  * Searches the index for the first slice overlapping a reference ID
-- * and position, or one immediately preceeding it if none is found in
-+ * and position, or one immediately preceding it if none is found in
-  * the index to overlap this position. (Our index may have missing
-  * entries, but we require at least one per reference.)
-  *
 --- python-pysam.orig/pysam/calignmentfile.pyx
 +++ python-pysam/pysam/calignmentfile.pyx
 @@ -1442,7 +1442,7 @@
diff --git a/debian/patches/ignore-htslib-dir.patch b/debian/patches/ignore-htslib-dir.patch
new file mode 100644
index 0000000..0a73343
--- /dev/null
+++ b/debian/patches/ignore-htslib-dir.patch
@@ -0,0 +1,27 @@
+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
+@@ -476,8 +476,6 @@
+     'url': "https://github.com/pysam-developers/pysam",
+     'packages': ['pysam',
+                  'pysam.include',
+-                 'pysam.include.htslib',
+-                 'pysam.include.htslib.htslib',
+                  'pysam.include.samtools',
+                  # 'pysam.include.samtools.bcftools',
+                  'pysam.include.samtools.win32'],
+@@ -493,7 +493,6 @@
+                     faidx],
+     'cmdclass': cmdclass,
+     'package_dir': {'pysam': 'pysam',
+-                    'pysam.include.htslib': 'htslib',
+                     'pysam.include.samtools': 'samtools'},
+     'package_data': {'': ['*.pxd', '*.h'], },
+     # do not pack in order to permit linking to csamtools.so
diff --git a/debian/patches/series b/debian/patches/series
index 73ffeaa..22c82d0 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
 change-htslib-statement-to-link-to-debian
 adding-include-hts-dirs
 correct-spelling-errors.patch
+ignore-htslib-dir.patch

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