Fix spelling typos, courtesy of lintian

Gbp-Pq: Name spelling

diff --git a/bcftools/filter.c b/bcftools/filter.c
index 02868c986965e1c92670d6f9acc05fd2dcf7a4ba..68705af1d3ee07de0cd39faf8bef21eaaf1f3cd9 100644 (file)
--- a/bcftools/filter.c
+++ b/bcftools/filter.c
@@ -993,7 +993,7 @@ static void filters_set_nmissing(filter_t *flt, bcf1_t *line, token_t *tok)
 }
 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);
 

diff --git a/bcftools/filter.c.pysam.c b/bcftools/filter.c.pysam.c
index 82c2b85977abb43e59f20882222dcfa2c35b47b1..fe4dda13d2e2eb3c6cf6302c28ca313a2ab37119 100644 (file)
--- a/bcftools/filter.c.pysam.c
+++ b/bcftools/filter.c.pysam.c
@@ -995,7 +995,7 @@ static void filters_set_nmissing(filter_t *flt, bcf1_t *line, token_t *tok)
 }
 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);
 

diff --git a/pysam/libcalignedsegment.pyx b/pysam/libcalignedsegment.pyx
index 7ad61ac25ac671c961f77fd2733c158a81afb999..2890dd16e6bcd0f25d5917383dbbc5346d06e59c 100644 (file)
--- a/pysam/libcalignedsegment.pyx
+++ b/pysam/libcalignedsegment.pyx
@@ -2244,7 +2244,7 @@ cdef class AlignedSegment:
         *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.

diff --git a/pysam/libcalignmentfile.pyx b/pysam/libcalignmentfile.pyx
index 4030868affdd8c11d1e9af0f688d6765a310aafa..ba20d0e7f5a0848ca97d1ddafbb8633b253130d0 100644 (file)
--- a/pysam/libcalignmentfile.pyx
+++ b/pysam/libcalignmentfile.pyx
@@ -1023,7 +1023,7 @@ cdef class AlignmentFile(HTSFile):
 
         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 @@ cdef class AlignmentFile(HTSFile):
         """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 @@ cdef class AlignmentFile(HTSFile):
 
         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 @@ cdef class AlignmentFile(HTSFile):
 
         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].
 

diff --git a/pysam/libchtslib.pxd b/pysam/libchtslib.pxd
index 8bcf399f36266ef4c2d07fb053a39d5392da5690..52d4bd0572980db14d93733cfb8c53f962576144 100644 (file)
--- a/pysam/libchtslib.pxd
+++ b/pysam/libchtslib.pxd
@@ -2502,7 +2502,7 @@ cdef extern from "htslib/cram.h" nogil:
     #         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)

diff --git a/pysam/libchtslib.pyx b/pysam/libchtslib.pyx
index c03c7cfab6d63302cdb8651071083b7a7c0504be..327b373ba6f3e8cbd193d11ae97ca12107bc3f26 100644 (file)
--- a/pysam/libchtslib.pyx
+++ b/pysam/libchtslib.pyx
@@ -587,7 +587,7 @@ cdef class HTSFile(object):
                 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 @@ cdef class HTSFile(object):
         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

diff --git a/pysam/libcutils.pyx b/pysam/libcutils.pyx
index 994a24009777bae6f6c873d04b58162dff8ae1c8..6857763add2cf387d854d42bb4147d439905afe1 100644 (file)
--- a/pysam/libcutils.pyx
+++ b/pysam/libcutils.pyx
@@ -179,7 +179,7 @@ cpdef parse_region(contig=None,
     `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.