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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
@@ -2238,7 +2238,7 @@
*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
@@ -1028,7 +1028,7 @@
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
@@ -1211,7 +1211,7 @@
"""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.
@@ -1360,7 +1360,7 @@
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.
@@ -1464,7 +1464,7 @@
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
@@ -2513,7 +2513,7 @@
# 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.
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