From 6543028fb24b9b665757d23d3e3da466793df245 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Wed, 16 Jan 2019 03:17:22 -0800 Subject: [PATCH] Fix lintian found spelling typos. --- debian/changelog | 1 + debian/patches/series | 1 + debian/patches/spelling | 115 ++++++++++++++++++++++++++++++++++++++++ 3 files changed, 117 insertions(+) create mode 100644 debian/patches/spelling diff --git a/debian/changelog b/debian/changelog index 0fe6487..bbca3fc 100644 --- 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 Wed, 16 Jan 2019 01:47:40 -0800 diff --git a/debian/patches/series b/debian/patches/series index 9a83180..d87fe71 100644 --- 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 index 0000000..579aa32 --- /dev/null +++ b/debian/patches/spelling @@ -0,0 +1,115 @@ +From: Michael R. Crusoe +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. -- 2.30.2