typos.patch: add; fix typos caught by lintian.

diff --git a/debian/patches/series b/debian/patches/series
index 43ee38595c16e3f1c81ef0d1514da8ca9eb787f0..d9e809a205d6a3e42f948ea0866fd91eb1f62bfd 100644 (file)
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
 skip_test_remote.patch
 clean_less
 skip-test-on-32-bit.patch
+typos.patch

diff --git a/debian/patches/typos.patch b/debian/patches/typos.patch
new file mode 100644 (file)
index 0000000..5201085
--- /dev/null
+++ b/debian/patches/typos.patch
@@ -0,0 +1,50 @@
+Description: fix typos caught by lintian.
+Author: Étienne Mollier <emollier@debian.org>
+Forwarded: https://github.com/pysam-developers/pysam/pull/1198
+Last-Update: 2023-06-23
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- python-pysam.orig/samtools/bam_ampliconclip.c
++++ python-pysam/samtools/bam_ampliconclip.c
+@@ -1014,7 +1014,7 @@
+ 
+     if (param.tol < 0) {
+         fprintf(stderr, "[ampliconclip] warning: invalid tolerance of %d,"
+-                        " reseting tolerance to default of 5.\n", param.tol);
++                        " resetting tolerance to default of 5.\n", param.tol);
+         param.tol = 5;
+     }
+ 
+--- python-pysam.orig/samtools/bam_ampliconclip.c.pysam.c
++++ python-pysam/samtools/bam_ampliconclip.c.pysam.c
+@@ -1016,7 +1016,7 @@
+ 
+     if (param.tol < 0) {
+         fprintf(samtools_stderr, "[ampliconclip] warning: invalid tolerance of %d,"
+-                        " reseting tolerance to default of 5.\n", param.tol);
++                        " resetting tolerance to default of 5.\n", param.tol);
+         param.tol = 5;
+     }
+ 
+--- python-pysam.orig/samtools/bamshuf.c
++++ python-pysam/samtools/bamshuf.c
+@@ -537,7 +537,7 @@
+             "      -l INT   Compression level [%d]\n" // DEF_CLEVEL
+             "      -n INT   Number of temporary files [%d]\n" // n_files
+             "      -T PREFIX\n"
+-            "               Write tempory files to PREFIX.nnnn.bam\n"
++            "               Write temporary files to PREFIX.nnnn.bam\n"
+             "      --no-PG  do not add a PG line\n",
+             reads_store, DEF_CLEVEL, n_files);
+ 
+--- python-pysam.orig/samtools/bamshuf.c.pysam.c
++++ python-pysam/samtools/bamshuf.c.pysam.c
+@@ -539,7 +539,7 @@
+             "      -l INT   Compression level [%d]\n" // DEF_CLEVEL
+             "      -n INT   Number of temporary files [%d]\n" // n_files
+             "      -T PREFIX\n"
+-            "               Write tempory files to PREFIX.nnnn.bam\n"
++            "               Write temporary files to PREFIX.nnnn.bam\n"
+             "      --no-PG  do not add a PG line\n",
+             reads_store, DEF_CLEVEL, n_files);
+