Fix spelling errors in source distribution (forwarded upstream as well)

diff --git a/debian/patches/correct-spelling-errors.patch b/debian/patches/correct-spelling-errors.patch
new file mode 100644 (file)
index 0000000..84e5644
--- /dev/null
+++ b/debian/patches/correct-spelling-errors.patch
@@ -0,0 +1,126 @@
+Description: Fix spelling errors in source distribution
+Author: Afif Elghraoui <afif@ghraoui.name>
+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 @@
+     .. note::
+ 
+         It is usually not necessary to create an object of this class
+-        explicitely. It is returned as a result of call to a
++        explicitly. It is returned as a result of call to a
+         :meth:`AlignmentFile.fetch`.
+ 
+     '''
+@@ -1491,7 +1491,7 @@
+     .. note::
+ 
+         It is usually not necessary to create an object of this class
+-        explicitely. It is returned as a result of call to a
++        explicitly. It is returned as a result of call to a
+         :meth:`AlignmentFile.fetch`.
+ 
+     """
+@@ -1645,7 +1645,7 @@
+ 
+     .. note::
+         It is usually not necessary to create an object of this class
+-        explicitely. It is returned as a result of call to a
++        explicitly. It is returned as a result of call to a
+         :meth:`AlignmentFile.fetch`.
+ 
+     """
+@@ -1715,7 +1715,7 @@
+ 
+     .. note::
+         It is usually not necessary to create an object of this class
+-        explicitely. It is returned as a result of call to a :meth:`AlignmentFile.fetch`.
++        explicitly. It is returned as a result of call to a :meth:`AlignmentFile.fetch`.
+     """
+ 
+     def __init__(self, AlignmentFile samfile, positions, int multiple_iterators=True):
+@@ -3311,7 +3311,7 @@
+         section.
+ 
+         *value_type* describes the type of *value* that is to entered
+-        into the alignment record.. It can be set explicitely to one
++        into the alignment record.. It can be set explicitly to one
+         of the valid one-letter type codes. If unset, an appropriate
+         type will be chosen automatically.
+ 
+@@ -3421,7 +3421,7 @@
+             bytesize, nvalues, values = convertBinaryTagToList(v + 1)
+             return values
+         else:
+-            raise ValueError("unknown auxilliary type '%s'" % auxtype)
++            raise ValueError("unknown auxiliary type '%s'" % auxtype)
+ 
+     def get_tags(self, with_value_type=False):
+         """the fields in the optional aligment section.
+@@ -3504,7 +3504,7 @@
+         a list of (tag, value) tuples.
+ 
+         The :term:`value type` of the values is determined from the
+-        python type. Optionally, a type may be given explicitely as
++        python type. Optionally, a type may be given explicitly as
+         a third value in the tuple, For example:
+ 
+         x.set_tags([(NM, 2, "i"), (RG, "GJP00TM04", "Z")]
+--- python-pysam.orig/pysam/ctabix.pyx
++++ python-pysam/pysam/ctabix.pyx
+@@ -199,7 +199,7 @@
+     +-----------+-----------+------------------------------------------+
+ 
+     Only the first three fields are required. Additional
+-    fields are optional, but if one is defined, all the preceeding
++    fields are optional, but if one is defined, all the preceding
+     need to be defined as well.
+ 
+     ''' 
+--- python-pysam.orig/save/pysam_test2.6.py
++++ python-pysam/save/pysam_test2.6.py
+@@ -355,7 +355,7 @@
+ 
+         If *use_template* is set, the header is copied from infile using the
+         template mechanism, otherwise target names and lengths are passed 
+-        explicitely. 
++        explicitly. 
+ 
+         '''
+ 
+--- python-pysam.orig/tests/AlignmentFile_test.py
++++ python-pysam/tests/AlignmentFile_test.py
+@@ -370,7 +370,7 @@
+ 
+         If *use_template* is set, the header is copied from infile
+         using the template mechanism, otherwise target names and
+-        lengths are passed explicitely.
++        lengths are passed explicitly.
+ 
+         The *checkf* is used to determine if the files are
+         equal.
+--- python-pysam.orig/tests/SamFile_test.py
++++ python-pysam/tests/SamFile_test.py
+@@ -355,7 +355,7 @@
+ 
+         If *use_template* is set, the header is copied from infile
+         using the template mechanism, otherwise target names and
+-        lengths are passed explicitely.
++        lengths are passed explicitly.
+ 
+         '''
+ 

diff --git a/debian/patches/series b/debian/patches/series
index 7de87be4dff6a9673ed18880184a71a80ebfbfd9..73ffeaa7320d148357db2dcb27d92c3a7d9d826b 100644 (file)
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
 change-htslib-statement-to-link-to-debian
 adding-include-hts-dirs
+correct-spelling-errors.patch