[med-svn] [Git][med-team/samtools][master] 2 commits: typos.patch: new patch.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sun Jun 18 22:28:46 BST 2023
Étienne Mollier pushed to branch master at Debian Med / samtools
Commits:
dddb318e by Étienne Mollier at 2023-06-18T23:25:58+02:00
typos.patch: new patch.
This fixes various typos caught by a few of the lintian parsers.
- - - - -
0fd429ba by Étienne Mollier at 2023-06-18T23:28:06+02:00
ready to upload to experimental.
- - - - -
3 changed files:
- debian/changelog
- debian/patches/series
- + debian/patches/typos.patch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-samtools (1.17-1) UNRELEASED; urgency=medium
+samtools (1.17-0+exp1) experimental; urgency=medium
* New upstream version (Closes: #1037431)
* Standards-Version: 4.6.2 (routine-update)
@@ -10,8 +10,10 @@ samtools (1.17-1) UNRELEASED; urgency=medium
This replaces the build dependency on libncurses5-dev, which is
flagged as obsolete by lintian.
* [7adec78] d/*.lintian-overrides: update mismatched override
+ * [dddb318] typos.patch: new patch.
+ This fixes various typos caught by a few of the lintian parsers.
- -- Étienne Mollier <emollier at debian.org> Mon, 12 Jun 2023 21:07:05 +0200
+ -- Étienne Mollier <emollier at debian.org> Sun, 18 Jun 2023 23:26:47 +0200
samtools (1.16.1-1) unstable; urgency=medium
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
reproducible.patch
samtools-fasta-q-whatis.patch
+typos.patch
=====================================
debian/patches/typos.patch
=====================================
@@ -0,0 +1,105 @@
+Description: fix various typos caught by various lintian parsers
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: no
+Last-Update: 2023-06-18
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- samtools.orig/doc/samtools-cram-size.1
++++ samtools/doc/samtools-cram-size.1
+@@ -85,7 +85,7 @@
+ G gzip-max Gzip -9
+ b bzip2 Bzip2
+ b bzip2-1 to bzip2-8 Explicit bzip2 compression levels
+-B bzip2-9 Bzip2 -9
++B bzip2-9 Bzip2 -9
+ l lzma LZMA
+ r r4x8-o0 rANS 4x8 Order-0
+ R r4x8-o1 rANS 4x8 Order-1
+@@ -159,7 +159,7 @@
+ BLOCK 12 1504781763 99158495 6.59% R QS
+ BLOCK 13 330065 84195 25.51% _r.g IN
+ BLOCK 14 26625602 6803930 25.55% Rrg SC
+-...
++[...]
+ .EE
+
+ .IP -
+@@ -178,7 +178,7 @@
+ BLOCK 14 23106404 5903351 25.55% r4x8-o1 SC
+ BLOCK 14 1951616 513722 26.32% r4x8-o0 SC
+ BLOCK 14 1567582 386857 24.68% gzip SC
+-...
++[...]
+ .EE
+
+ .IP -
+@@ -195,12 +195,12 @@
+ SC BYTE_ARRAY_STOP(stop=0,id=14)
+ BB BYTE_ARRAY_LEN(len_codec={EXTERNAL(id=42)}, \\
+ val_codec={EXTERNAL(id=37)}
+- ...
++ [...]
+ XAZ BYTE_ARRAY_STOP(stop=9,id=5783898)
+ MDZ BYTE_ARRAY_STOP(stop=9,id=5063770)
+ ASC BYTE_ARRAY_LEN(len_codec={HUFFMAN(codes={1},lengths={0})}, \\
+ val_codec={EXTERNAL(id=4281155)}
+- ...
++ [...]
+ .EE
+
+ .SH AUTHOR
+--- samtools.orig/bam_ampliconclip.c
++++ 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;
+ }
+
+--- samtools.orig/bamshuf.c
++++ 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);
+
+--- samtools.orig/doc/samtools-merge.1
++++ samtools/doc/samtools-merge.1
+@@ -94,7 +94,7 @@
+ information. Additionally many files being read from simultaneously
+ may cause a certain amount of "disk thrashing". To partially
+ alleviate this the merge command will load 1MB of data at a time from
+-each file, but this in turn adds to the overal merge program memory
++each file, but this in turn adds to the overall merge program memory
+ usage. Please take this into account when setting memory limits.
+
+ In extreme cases, it may be necessary to reduce the problem to fewer
+--- samtools.orig/doc/samtools-reset.1
++++ samtools/doc/samtools-reset.1
+@@ -97,7 +97,7 @@
+
+ .TP 8
+ .BI --no-RG
+-RG lines in input will be discarded with this option. By default, RG lines will be present in ouput.
++RG lines in input will be discarded with this option. By default, RG lines will be present in output.
+
+ With this option, RG aux tags will also be discarded.
+
+--- samtools.orig/doc/samtools-samples.1
++++ samtools/doc/samtools-samples.1
+@@ -122,7 +122,7 @@
+ \&. example.sam N
+ .EE
+ .IP o 2
+-print wether the files are indexed using custom bai files.
++print whether the files are indexed using custom bai files.
+ .EX 2
+ $ samtools samples -i -h -X S1.bam S2.bam S1.bam.bai S2.bam.bai
+ #SM PATH INDEX
View it on GitLab: https://salsa.debian.org/med-team/samtools/-/compare/1cc8cf9883be110a933313d336474387820cfcf0...0fd429ba6a0ba10b3661c1ef15209c9422eaed8b
--
View it on GitLab: https://salsa.debian.org/med-team/samtools/-/compare/1cc8cf9883be110a933313d336474387820cfcf0...0fd429ba6a0ba10b3661c1ef15209c9422eaed8b
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