[med-svn] [Git][med-team/sortmerna][master] 4 commits: d/rules: convert example files to Unicode per lintian flag.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sat Jan 7 16:43:56 GMT 2023
Étienne Mollier pushed to branch master at Debian Med / sortmerna
Commits:
b7b49153 by Étienne Mollier at 2023-01-07T17:41:38+01:00
d/rules: convert example files to Unicode per lintian flag.
- - - - -
8425065a by Étienne Mollier at 2023-01-07T17:42:01+01:00
typos.patch: add; fix typos caught by lintian.
- - - - -
27899403 by Étienne Mollier at 2023-01-07T17:42:29+01:00
d/copyright: update copyright year.
- - - - -
376f5e91 by Étienne Mollier at 2023-01-07T17:43:19+01:00
initialise changelog
- - - - -
5 changed files:
- debian/changelog
- debian/copyright
- debian/patches/series
- + debian/patches/typos.patch
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+sortmerna (4.3.6-3) UNRELEASED; urgency=medium
+
+ * d/rules: convert example files to Unicode per lintian flag.
+ * typos.patch: add; fix typos caught by lintian.
+ * d/copyright: update copyright year.
+
+ -- Étienne Mollier <emollier at debian.org> Sat, 07 Jan 2023 17:42:57 +0100
+
sortmerna (4.3.6-2) unstable; urgency=medium
* d/rules: remove dh_clean override; not needed anymore.
=====================================
debian/copyright
=====================================
@@ -36,7 +36,8 @@ License: PublicDomain
Files: debian/*
Copyright: 2015 Tim Booth <tbooth at ceh.ac.uk>
- 2015 Andreas Tille <tille at debian.org>
+ 2015-2022 Andreas Tille <tille at debian.org>
+ 2023 Étienne Mollier <emollier at debian.org>
License: LGPL-3+
Files: src/sortmerna/ssw.c
=====================================
debian/patches/series
=====================================
@@ -2,3 +2,4 @@ cmake_RocksDB.patch
rapidjson.patch
concurrentqueue.h.patch
no_static_linking.patch
+typos.patch
=====================================
debian/patches/typos.patch
=====================================
@@ -0,0 +1,57 @@
+Description: fix typos caught by lintian.
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: no
+Last-Update: 2023-01-07
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- sortmerna.orig/3rdparty/cmph/brz.c
++++ sortmerna/3rdparty/cmph/brz.c
+@@ -152,7 +152,7 @@
+ // Clustering the keys by graph id.
+ if (mph->verbosity)
+ {
+- fprintf(stderr, "Partioning the set of keys.\n");
++ fprintf(stderr, "Partitioning the set of keys.\n");
+ }
+
+ while(1)
+--- sortmerna.orig/ChangeLog
++++ sortmerna/ChangeLog
+@@ -47,7 +47,7 @@
+ 15 August 2014
+ - [affects Installation] added script `build.sh` to call configure, touch commands and make in order to avoid timestamp issues when cloning this repository
+ 21 August 2014
+- - [affects OTU-picking using "--otu_map --best INT" where INT > 1] changed the read_hits_align_info structure from map<uint32_t,pair<uint16_t,s_align*> > to map<uint32_t, triple_s > where the structure triple_s holds two uint16_t variables and an s_align* variable. This allows to store an additional integer for giving the index in s_align array of the highest scoring alignment. This is necessary if —otu_map and —best [INT] options are used where INT > 1 since different OTU ids can be used in the OTU-map when multiple alignments score equally as well. To illustrate an example,
++ - [affects OTU-picking using "--otu_map --best INT" where INT > 1] changed the read_hits_align_info structure from map<uint32_t,pair<uint16_t,s_align*> > to map<uint32_t, triple_s > where the structure triple_s holds two uint16_t variables and an s_align* variable. This allows one to store an additional integer for giving the index in s_align array of the highest scoring alignment. This is necessary if —otu_map and —best [INT] options are used where INT > 1 since different OTU ids can be used in the OTU-map when multiple alignments score equally as well. To illustrate an example,
+
+ (a) —best 1, the s_align array is size 1 and only the single best alignment is stored, being the first encountered alignment if multiple alignments of equal score are found.
+ (b) —best 4, the s_align array is size 4. Assume the first 2 alignments score 144 (occupying the first 2 slots on s_align array) and the next 3 alignments score 197 (2 of these alignments will occupy the final 2 slots, where the 3rd alignment will overwrite the first slot holding 144). We will have a situation like: 197, 144, 197, 197. In order to follow the same principle of (a) where the first encountered alignment of the highest score is output, we need to know that this alignment was in slot 3 (not slot 1).
+--- sortmerna.orig/include/options.hpp
++++ sortmerna/include/options.hpp
+@@ -121,7 +121,7 @@
+ " -------------------------------------------------------------------------------------------------------------\n",
+ help_ref =
+ "Reference file (FASTA) absolute or relative path.\n\n"
+- " Use mutliple times, once per a reference file\n\n",
++ " Use multiple times, once per a reference file\n\n",
+ help_reads =
+ "Raw reads file (FASTA/FASTQ/FASTA.GZ/FASTQ.GZ).\n\n"
+ " Use twice for files with paired reads.\n"
+@@ -198,7 +198,7 @@
+ help_num_alignments =
+ "Positive integer (INT >=0).\n\n"
+ " If used with '-" + OPT_NO_BEST + "' reports first INT alignments per read reaching\n"
+- " E-value threshold, which allows to lower the CPU time and memory use.\n"
++ " E-value threshold, which allows one to lower the CPU time and memory use.\n"
+ " Otherwise outputs INT best alignments.\n"
+ " If INT = 0, all alignments are output\n\n",
+
+@@ -367,7 +367,7 @@
+ "Controls the output compression '-1'\n\n"
+ " By default the report files are produced in the same format as the input i.e.\n"
+ " if the reads files are compressed (gz), the output is also compressed.\n"
+- " The default behaviour can be overriden by using '-" + OPT_ZIP_OUT + "'.\n"
++ " The default behaviour can be overridden by using '-" + OPT_ZIP_OUT + "'.\n"
+ " The possible values: '1/true/t/yes/y'\n"
+ " '0/false/f/no/n'\n"
+ " '-1' (the same format as input - default)\n"
=====================================
debian/rules
=====================================
@@ -5,6 +5,7 @@
export DEB_BUILD_MAINT_OPTIONS=hardening=+all
export CMAKE_PREFIX_PATH=/usr/lib/$(DEB_HOST_MULTIARCH)/cmake/
+DTMP=$(CURDIR)/debian/sortmerna
# In this particular instance, building with sse2 support is not an
# architecture baseline violation for the i386 release architecture, because
@@ -20,6 +21,16 @@ endif
execute_after_dh_install:
find debian -name cmake -type d | xargs rm -rvf
+execute_after_dh_installexamples:
+ # Convert example files to Unicode.
+ set -e \
+ ; cd $(CURDIR)/tests/sortmerna/ \
+ ; for cxxfile in *.cpp \
+ ; do iconv -f ISO-8859-15 -t UTF-8 \
+ < $${cxxfile} \
+ > $(DTMP)/usr/share/doc/sortmerna/examples/$${cxxfile} \
+ ; done
+
execute_after_dh_fixperms:
find debian/sortmerna -name '*.sh' -exec chmod -v +x '{}' ';'
find debian/sortmerna -name '*.py' -exec chmod -v -x '{}' ';'
View it on GitLab: https://salsa.debian.org/med-team/sortmerna/-/compare/cc984575ddd479ac9745a7877dbc102f7141df57...376f5e91da83105dd0d817d8cc81f56ce619777d
--
View it on GitLab: https://salsa.debian.org/med-team/sortmerna/-/compare/cc984575ddd479ac9745a7877dbc102f7141df57...376f5e91da83105dd0d817d8cc81f56ce619777d
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