Fix lintian found spelling typos.

diff --git a/debian/changelog b/debian/changelog
index 0fe648772911bc5f82483fa3f9971842f6aa5133..bbca3fc01e74e1411452d6992a3c9bcdcb006781 100644 (file)
--- a/debian/changelog
+++ b/debian/changelog
@@ -4,6 +4,7 @@ python-pysam (0.15.2+ds-1) UNRELEASED; urgency=medium
   * New upstream version
   * Standards-Version: 4.3.0, no changes needed
   * added Py2 and Py3 versions of ${python:Provides}
+  * Fix lintian found spelling typos.
 
  -- Michael R. Crusoe <michael.crusoe@gmail.com>  Wed, 16 Jan 2019 01:47:40 -0800
 

diff --git a/debian/patches/series b/debian/patches/series
index 9a831802894f96b5d09c2a859b5b5494f65dca86..d87fe71f354b58d4a8fb2d7dd7f04d8880cbb989 100644 (file)
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
 skip_test_remote.patch
 skip_test_needing_missing_data.patch
+spelling

diff --git a/debian/patches/spelling b/debian/patches/spelling
new file mode 100644 (file)
index 0000000..579aa32
--- /dev/null
+++ b/debian/patches/spelling
@@ -0,0 +1,115 @@
+From: Michael R. Crusoe <michael.crusoe@gmail.com>
+Subject: Fix spelling typos, courtesy of lintian
+--- python-pysam.orig/bcftools/filter.c
++++ python-pysam/bcftools/filter.c
+@@ -993,7 +993,7 @@
+ }
+ static int func_npass(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+ {
+-    if ( nstack==0 ) error("Error parsing the expresion\n");
++    if ( nstack==0 ) error("Error parsing the expression\n");
+     token_t *tok = stack[nstack - 1];
+     if ( !tok->nsamples ) error("The function %s works with FORMAT fields\n", rtok->tag);
+ 
+--- python-pysam.orig/bcftools/filter.c.pysam.c
++++ python-pysam/bcftools/filter.c.pysam.c
+@@ -995,7 +995,7 @@
+ }
+ static int func_npass(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+ {
+-    if ( nstack==0 ) error("Error parsing the expresion\n");
++    if ( nstack==0 ) error("Error parsing the expression\n");
+     token_t *tok = stack[nstack - 1];
+     if ( !tok->nsamples ) error("The function %s works with FORMAT fields\n", rtok->tag);
+ 
+--- python-pysam.orig/pysam/libcalignedsegment.pyx
++++ python-pysam/pysam/libcalignedsegment.pyx
+@@ -2244,7 +2244,7 @@
+         *value*.
+ 
+         An existing value of the same *tag* will be overwritten unless
+-        *replace* is set to False. This is usually not recommened as a
++        *replace* is set to False. This is usually not recommended as a
+         tag may only appear once in the optional alignment section.
+ 
+         If *value* is None, the tag will be deleted.
+--- python-pysam.orig/pysam/libcalignmentfile.pyx
++++ python-pysam/pysam/libcalignmentfile.pyx
+@@ -1023,7 +1023,7 @@
+ 
+         See :meth:`~pysam.HTSFile.parse_region` for more information
+         on how genomic regions can be specified. :term:`reference` and
+-        `end` are also accepted for backward compatiblity as synonyms
++        `end` are also accepted for backward compatibility as synonyms
+         for :term:`contig` and `stop`, respectively.
+ 
+         Without a `contig` or `region` all mapped reads in the file
+@@ -1206,7 +1206,7 @@
+         """perform a :term:`pileup` within a :term:`region`. The region is
+         specified by :term:`contig`, `start` and `stop` (using
+         0-based indexing).  :term:`reference` and `end` are also accepted for
+-        backward compatiblity as synonyms for :term:`contig` and `stop`,
++        backward compatibility as synonyms for :term:`contig` and `stop`,
+         respectively.  Alternatively, a samtools 'region' string
+         can be supplied.
+ 
+@@ -1355,7 +1355,7 @@
+ 
+         The region is specified by :term:`contig`, `start` and `stop`.
+         :term:`reference` and `end` are also accepted for backward
+-        compatiblity as synonyms for :term:`contig` and `stop`,
++        compatibility as synonyms for :term:`contig` and `stop`,
+         respectively.  Alternatively, a :term:`samtools` :term:`region`
+         string can be supplied.
+ 
+@@ -1459,7 +1459,7 @@
+ 
+         The region is specified by :term:`contig`, `start` and `stop`.
+         :term:`reference` and `end` are also accepted for backward
+-        compatiblity as synonyms for :term:`contig` and `stop`,
++        compatibility as synonyms for :term:`contig` and `stop`,
+         respectively.  Alternatively, a :term:`samtools` :term:`region`
+         string can be supplied.  The coverage is computed per-base [ACGT].
+ 
+--- python-pysam.orig/pysam/libchtslib.pxd
++++ python-pysam/pysam/libchtslib.pxd
+@@ -2502,7 +2502,7 @@
+     #         2 if the file is a stream and thus unseekable
+     #         1 if the file contains an EOF block
+     #         0 if the file does not contain an EOF block
+-    #        -1 if an error occured whilst reading the file or we could not seek back to where we were
++    #        -1 if an error occurred whilst reading the file or we could not seek back to where we were
+     #
+     #
+     int cram_check_EOF(cram_fd *fd)
+--- python-pysam.orig/pysam/libchtslib.pyx
++++ python-pysam/pysam/libchtslib.pyx
+@@ -587,7 +587,7 @@
+                 rval = hts_opt_apply(self.htsfile, opts)
+                 if rval != 0:
+                     hts_opt_free(opts)
+-                    raise RuntimeError('An error occured while applying the requested format options')
++                    raise RuntimeError('An error occurred while applying the requested format options')
+                 hts_opt_free(opts)
+ 
+     def parse_region(self, contig=None, start=None, stop=None,
+@@ -597,7 +597,7 @@
+         either be specified by :term:`contig`, `start` and
+         `stop`. `start` and `stop` denote 0-based, half-open
+         intervals. :term:`reference` and `end` are also accepted for
+-        backward compatiblity as synonyms for :term:`contig` and
++        backward compatibility as synonyms for :term:`contig` and
+         `stop`, respectively.
+ 
+         Alternatively, a samtools :term:`region` string can be
+--- python-pysam.orig/pysam/libcutils.pyx
++++ python-pysam/pysam/libcutils.pyx
+@@ -179,7 +179,7 @@
+     `end`. `start` and `end` denote 0-based, half-open intervals.
+     
+     :term:`reference` and `end` are also accepted for backward
+-    compatiblity as synonyms for :term:`contig` and `stop`,
++    compatibility as synonyms for :term:`contig` and `stop`,
+     respectively.
+ 
+     Alternatively, a samtools :term:`region` string can be supplied.