From 47981ea58b04733ab494f3c6d3dbf296fbf556fa Mon Sep 17 00:00:00 2001 From: Afif Elghraoui Date: Mon, 23 Jan 2017 19:13:33 -0800 Subject: [PATCH] Update patches --- debian/patches/rpath.patch | 8 +-- debian/patches/series | 1 - debian/patches/spelling.patch | 91 ----------------------------------- 3 files changed, 4 insertions(+), 96 deletions(-) delete mode 100644 debian/patches/spelling.patch diff --git a/debian/patches/rpath.patch b/debian/patches/rpath.patch index d9d699a..44a34aa 100644 --- a/debian/patches/rpath.patch +++ b/debian/patches/rpath.patch @@ -4,7 +4,7 @@ Forwarded: not-needed Last-Update: 2016-03-05 --- python-pysam.orig/cy_build.py +++ python-pysam/cy_build.py -@@ -53,7 +53,7 @@ +@@ -57,7 +57,7 @@ ext._init_func(ext) if not self.inplace: @@ -12,8 +12,8 @@ Last-Update: 2016-03-05 + pass if sys.platform == 'darwin': - -@@ -82,6 +82,5 @@ + relative_module_path = ext.name.replace(".", os.sep) + get_config_vars()["SO"] +@@ -85,6 +85,5 @@ if not ext.extra_link_args: ext.extra_link_args = [] @@ -22,7 +22,7 @@ Last-Update: 2016-03-05 build_ext.build_extension(self, ext) --- python-pysam.orig/setup.py +++ python-pysam/setup.py -@@ -349,7 +349,6 @@ +@@ -353,7 +353,6 @@ shared_htslib_sources + os_c_files, library_dirs=htslib_library_dirs, diff --git a/debian/patches/series b/debian/patches/series index e4e47fe..da8b790 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,2 +1 @@ rpath.patch -spelling.patch diff --git a/debian/patches/spelling.patch b/debian/patches/spelling.patch deleted file mode 100644 index 6a1be87..0000000 --- a/debian/patches/spelling.patch +++ /dev/null @@ -1,91 +0,0 @@ -From 947f6eb4d612d6986ef705ca6968ff841d7f3d16 Mon Sep 17 00:00:00 2001 -From: Afif Elghraoui -Date: Sat, 23 Jul 2016 18:34:54 -0700 -Subject: [PATCH] Fix spelling/grammar issues found using Debian QA tools - ---- - bcftools/vcfisec.c | 2 +- - bcftools/vcfisec.c.pysam.c | 2 +- - pysam/calignedsegment.pyx | 10 +++++----- - pysam/calignmentfile.pyx | 2 +- - 4 files changed, 8 insertions(+), 8 deletions(-) - -diff --git a/bcftools/vcfisec.c b/bcftools/vcfisec.c -index 9afe620..9eb3a7c 100644 ---- a/bcftools/vcfisec.c -+++ b/bcftools/vcfisec.c -@@ -317,7 +317,7 @@ static void init_data(args_t *args) - while (*p && *p!=',') p++; - if ( *p==',' ) p++; - } -- if ( args->nwrite>1 && !args->prefix ) error("Expected -p when mutliple output files given: --write %s\n", args->write_files); -+ if ( args->nwrite>1 && !args->prefix ) error("Expected -p when multiple output files given: --write %s\n", args->write_files); - if ( args->isec_op==OP_COMPLEMENT && args->nwrite ) - { - if ( args->nwrite>1 ) error("Multiple files to -w make no sense with -C\n"); -diff --git a/bcftools/vcfisec.c.pysam.c b/bcftools/vcfisec.c.pysam.c -index 758d475..e3890d5 100644 ---- a/bcftools/vcfisec.c.pysam.c -+++ b/bcftools/vcfisec.c.pysam.c -@@ -319,7 +319,7 @@ static void init_data(args_t *args) - while (*p && *p!=',') p++; - if ( *p==',' ) p++; - } -- if ( args->nwrite>1 && !args->prefix ) error("Expected -p when mutliple output files given: --write %s\n", args->write_files); -+ if ( args->nwrite>1 && !args->prefix ) error("Expected -p when multiple output files given: --write %s\n", args->write_files); - if ( args->isec_op==OP_COMPLEMENT && args->nwrite ) - { - if ( args->nwrite>1 ) error("Multiple files to -w make no sense with -C\n"); -diff --git a/pysam/calignedsegment.pyx b/pysam/calignedsegment.pyx -index f4e0750..0f457ae 100644 ---- a/pysam/calignedsegment.pyx -+++ b/pysam/calignedsegment.pyx -@@ -775,7 +775,7 @@ cdef class AlignedSegment: - ---------- - - htsfile -- AlignmentFile object to map numerical -- identifers to chromosome names. -+ identifiers to chromosome names. - """ - - cdef kstring_t line -@@ -2288,7 +2288,7 @@ cdef class AlignedSegment: - - - cdef class PileupColumn: -- '''A pileup of reads at a particular reference sequence postion -+ '''A pileup of reads at a particular reference sequence position - (:term:`column`). A pileup column contains all the reads that map - to a certain target base. - -@@ -2416,11 +2416,11 @@ cdef class PileupRead: - return self._qpos - - property indel: -- """indel length for the position follwing the current pileup site. -+ """indel length for the position following the current pileup site. - - This quantity peeks ahead to the next cigar operation in this -- alignment. If the next operation is and insertion, indel will -- be positve. If the next operation is a deletion, it will be -+ alignment. If the next operation is an insertion, indel will -+ be positive. If the next operation is a deletion, it will be - negation. 0 if the next operation is not an indel. - - """ -diff --git a/pysam/calignmentfile.pyx b/pysam/calignmentfile.pyx -index ed5e584..f6abe6b 100644 ---- a/pysam/calignmentfile.pyx -+++ b/pysam/calignmentfile.pyx -@@ -1055,7 +1055,7 @@ cdef class AlignmentFile: - ---------- - - stepper : string -- The stepper controlls how the iterator advances. -+ The stepper controls how the iterator advances. - Possible options for the stepper are - - ``all`` --- -2.1.4 - -- 2.30.2