Update patches

diff --git a/debian/patches/rpath.patch b/debian/patches/rpath.patch
index d9d699a0796c873306264675156f2fc4787824b2..44a34aa23ae315857714aac04a679f0dd19ecf66 100644 (file)
--- a/debian/patches/rpath.patch
+++ b/debian/patches/rpath.patch
@@ -4,7 +4,7 @@ Forwarded: not-needed
 Last-Update: 2016-03-05
 --- python-pysam.orig/cy_build.py
 +++ python-pysam/cy_build.py
-@@ -53,7 +53,7 @@
+@@ -57,7 +57,7 @@
              ext._init_func(ext)
  
          if not self.inplace:
@@ -12,8 +12,8 @@ Last-Update: 2016-03-05
 +            pass
  
          if sys.platform == 'darwin':
- 
-@@ -82,6 +82,5 @@
+             relative_module_path = ext.name.replace(".", os.sep) + get_config_vars()["SO"]
+@@ -85,6 +85,5 @@
              if not ext.extra_link_args:
                  ext.extra_link_args = []
  
@@ -22,7 +22,7 @@ Last-Update: 2016-03-05
          build_ext.build_extension(self, ext)
 --- python-pysam.orig/setup.py
 +++ python-pysam/setup.py
-@@ -349,7 +349,6 @@
+@@ -353,7 +353,6 @@
      shared_htslib_sources +
      os_c_files,
      library_dirs=htslib_library_dirs,

diff --git a/debian/patches/series b/debian/patches/series
index e4e47fe4d7297626818d74211cb648504fd4c5c5..da8b79080b4d9bdb52ef264ac43f936283f0956a 100644 (file)
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1 @@
 rpath.patch
-spelling.patch

diff --git a/debian/patches/spelling.patch b/debian/patches/spelling.patch
deleted file mode 100644 (file)
index 6a1be87..0000000
--- a/debian/patches/spelling.patch
+++ /dev/null
@@ -1,91 +0,0 @@
-From 947f6eb4d612d6986ef705ca6968ff841d7f3d16 Mon Sep 17 00:00:00 2001
-From: Afif Elghraoui <afif@debian.org>
-Date: Sat, 23 Jul 2016 18:34:54 -0700
-Subject: [PATCH] Fix spelling/grammar issues found using Debian QA tools
-
----
- bcftools/vcfisec.c         |  2 +-
- bcftools/vcfisec.c.pysam.c |  2 +-
- pysam/calignedsegment.pyx  | 10 +++++-----
- pysam/calignmentfile.pyx   |  2 +-
- 4 files changed, 8 insertions(+), 8 deletions(-)
-
-diff --git a/bcftools/vcfisec.c b/bcftools/vcfisec.c
-index 9afe620..9eb3a7c 100644
---- a/bcftools/vcfisec.c
-+++ b/bcftools/vcfisec.c
-@@ -317,7 +317,7 @@ static void init_data(args_t *args)
-         while (*p && *p!=',') p++;
-         if ( *p==',' ) p++;
-     }
--    if ( args->nwrite>1 && !args->prefix ) error("Expected -p when mutliple output files given: --write %s\n", args->write_files);
-+    if ( args->nwrite>1 && !args->prefix ) error("Expected -p when multiple output files given: --write %s\n", args->write_files);
-     if ( args->isec_op==OP_COMPLEMENT && args->nwrite )
-     {
-         if ( args->nwrite>1 ) error("Multiple files to -w make no sense with -C\n");
-diff --git a/bcftools/vcfisec.c.pysam.c b/bcftools/vcfisec.c.pysam.c
-index 758d475..e3890d5 100644
---- a/bcftools/vcfisec.c.pysam.c
-+++ b/bcftools/vcfisec.c.pysam.c
-@@ -319,7 +319,7 @@ static void init_data(args_t *args)
-         while (*p && *p!=',') p++;
-         if ( *p==',' ) p++;
-     }
--    if ( args->nwrite>1 && !args->prefix ) error("Expected -p when mutliple output files given: --write %s\n", args->write_files);
-+    if ( args->nwrite>1 && !args->prefix ) error("Expected -p when multiple output files given: --write %s\n", args->write_files);
-     if ( args->isec_op==OP_COMPLEMENT && args->nwrite )
-     {
-         if ( args->nwrite>1 ) error("Multiple files to -w make no sense with -C\n");
-diff --git a/pysam/calignedsegment.pyx b/pysam/calignedsegment.pyx
-index f4e0750..0f457ae 100644
---- a/pysam/calignedsegment.pyx
-+++ b/pysam/calignedsegment.pyx
-@@ -775,7 +775,7 @@ cdef class AlignedSegment:
-         ----------
- 
-         htsfile -- AlignmentFile object to map numerical
--                   identifers to chromosome names.
-+                   identifiers to chromosome names.
-         """
- 
-         cdef kstring_t line
-@@ -2288,7 +2288,7 @@ cdef class AlignedSegment:
- 
- 
- cdef class PileupColumn:
--    '''A pileup of reads at a particular reference sequence postion
-+    '''A pileup of reads at a particular reference sequence position
-     (:term:`column`). A pileup column contains all the reads that map
-     to a certain target base.
- 
-@@ -2416,11 +2416,11 @@ cdef class PileupRead:
-             return self._qpos
- 
-     property indel:
--        """indel length for the position follwing the current pileup site.
-+        """indel length for the position following the current pileup site.
- 
-         This quantity peeks ahead to the next cigar operation in this
--        alignment. If the next operation is and insertion, indel will
--        be positve. If the next operation is a deletion, it will be
-+        alignment. If the next operation is an insertion, indel will
-+        be positive. If the next operation is a deletion, it will be
-         negation. 0 if the next operation is not an indel.
- 
-         """
-diff --git a/pysam/calignmentfile.pyx b/pysam/calignmentfile.pyx
-index ed5e584..f6abe6b 100644
---- a/pysam/calignmentfile.pyx
-+++ b/pysam/calignmentfile.pyx
-@@ -1055,7 +1055,7 @@ cdef class AlignmentFile:
-         ----------
- 
-         stepper : string
--           The stepper controlls how the iterator advances.
-+           The stepper controls how the iterator advances.
-            Possible options for the stepper are
- 
-            ``all``
--- 
-2.1.4
-