From d2473114c4126b1bbd74702a0686ad29497ef41b Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Wed, 20 Feb 2019 10:45:47 +0000 Subject: [PATCH] Fix spelling typos, courtesy of lintian Gbp-Pq: Name spelling --- bcftools/filter.c | 2 +- bcftools/filter.c.pysam.c | 2 +- pysam/libcalignedsegment.pyx | 2 +- pysam/libcalignmentfile.pyx | 8 ++++---- pysam/libchtslib.pxd | 2 +- pysam/libchtslib.pyx | 4 ++-- pysam/libcutils.pyx | 2 +- 7 files changed, 11 insertions(+), 11 deletions(-) diff --git a/bcftools/filter.c b/bcftools/filter.c index 02868c9..68705af 100644 --- 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 82c2b85..fe4dda1 100644 --- 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 7ad61ac..2890dd1 100644 --- 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 4030868..ba20d0e 100644 --- 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 8bcf399..52d4bd0 100644 --- 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 c03c7cf..327b373 100644 --- 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 994a240..6857763 100644 --- 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. -- 2.30.2