Fix spelling issues (forwarded)

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

diff --git a/debian/patches/spelling.patch b/debian/patches/spelling.patch
new file mode 100644 (file)
index 0000000..6a1be87
--- /dev/null
+++ b/debian/patches/spelling.patch
@@ -0,0 +1,91 @@
+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
+