[med-svn] [Git][med-team/mapsembler2][master] 5 commits: d/control: updated uploader address
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Fri Jul 2 23:13:52 BST 2021
Étienne Mollier pushed to branch master at Debian Med / mapsembler2
Commits:
f85e2080 by Étienne Mollier at 2021-07-02T23:58:41+02:00
d/control: updated uploader address
- - - - -
eab15b8d by Étienne Mollier at 2021-07-02T23:59:38+02:00
d/control: standard version 4.5.1
- - - - -
b683a5eb by Étienne Mollier at 2021-07-03T00:08:58+02:00
d/mans/mapsembler2_kissreads.1
fix typo-in-manual-page
- - - - -
5cfb5a87 by Étienne Mollier at 2021-07-03T00:10:09+02:00
spelling.patch: fix spelling-error-in-binary
- - - - -
df74cc12 by Étienne Mollier at 2021-07-03T00:11:44+02:00
update changelog
- - - - -
4 changed files:
- debian/changelog
- debian/control
- debian/mans/mapsembler2_kissreads.1
- debian/patches/spelling.patch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,8 +1,12 @@
mapsembler2 (2.2.4+dfsg1-4) UNRELEASED; urgency=medium
* d/salsa-ci.yml: disable i386 build and reprotest in Salsa CI
+ * d/control: updated uploader address
+ * d/control: standard version 4.5.1
+ * d/mans/mapsembler2_kissreads.1: fix typo-in-manual-page
+ * spelling.patch: fix spelling-error-in-binary
- -- Étienne Mollier <etienne.mollier at mailoo.org> Sun, 21 Feb 2021 15:25:45 +0100
+ -- Étienne Mollier <emollier at debian.org> Sat, 03 Jul 2021 00:10:43 +0200
mapsembler2 (2.2.4+dfsg1-3) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -2,7 +2,7 @@ Source: mapsembler2
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Olivier Sallou <osallou at debian.org>,
Andreas Tille <tille at debian.org>,
- Étienne Mollier <etienne.mollier at mailoo.org>
+ Étienne Mollier <emollier at debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
@@ -12,7 +12,7 @@ Build-Depends: debhelper-compat (= 13),
libhdf5-dev,
libcppunit-dev,
libboost-dev
-Standards-Version: 4.5.0
+Standards-Version: 4.5.1
Vcs-Browser: https://salsa.debian.org/med-team/mapsembler2
Vcs-Git: https://salsa.debian.org/med-team/mapsembler2.git
Homepage: http://colibread.inria.fr/mapsembler2/
=====================================
debian/mans/mapsembler2_kissreads.1
=====================================
@@ -34,7 +34,7 @@ Any other situation (s not coherent with any): couple non read coherent, not out
.HP
\fB\-n\fR the input file (toCheck.fasta) is a kissnp output (incompatible with \fB\-I\fR option)
.IP
-in this case: 1/ only the upper characters are considered (no mapping done on the extensions) and 2/ the central position (where the SNP occurs) is strictly mapped, no subsitution is authorized on this position.
+in this case: 1/ only the upper characters are considered (no mapping done on the extensions) and 2/ the central position (where the SNP occurs) is strictly mapped, no substitution is authorized on this position.
.HP
\fB\-I\fR the input file (toCheck.fasta) is an Intl output (incompatible with \fB\-n\fR option)
.HP
=====================================
debian/patches/spelling.patch
=====================================
@@ -2,9 +2,9 @@ Description: Fix spelling
Author: Andreas Tille <tille at debian.org>
Last-Update: Wed, 10 Oct 2018 12:49:34 +0200
---- a/kissreads_graph/KissReadsGraph.cpp
-+++ b/kissreads_graph/KissReadsGraph.cpp
-@@ -35,7 +35,7 @@ void print_usage_and_exit(char * name){
+--- mapsembler2.orig/kissreads_graph/KissReadsGraph.cpp
++++ mapsembler2/kissreads_graph/KissReadsGraph.cpp
+@@ -35,7 +35,7 @@
fprintf (stderr, "With option \"-t modify\": outputs the same simplified graph:\n");
fprintf (stderr, "\t removing low covered edges and nodes (less that min_coverage)\n");
fprintf (stderr, "\t then phasing simple non branching paths\n");
@@ -13,9 +13,9 @@ Last-Update: Wed, 10 Oct 2018 12:49:34 +0200
fprintf (stderr, "\nMANDATORY\n");
---- a/mapsembler2_extend/IterativeExtensions.cpp
-+++ b/mapsembler2_extend/IterativeExtensions.cpp
-@@ -178,7 +178,7 @@ void IterativeExtensions::construct_line
+--- mapsembler2.orig/mapsembler2_extend/IterativeExtensions.cpp
++++ mapsembler2/mapsembler2_extend/IterativeExtensions.cpp
+@@ -178,7 +178,7 @@
revcomp_sequence(kmer_seq,sizeKmer);
if (debug)
@@ -24,7 +24,7 @@ Last-Update: Wed, 10 Oct 2018 12:49:34 +0200
// right extension
int len_right = traversal->traverse(kmer,right_traversal,strand);
-@@ -397,7 +397,7 @@ void IterativeExtensions::construct_line
+@@ -397,7 +397,7 @@
revcomp_sequence(kmer_seq,sizeKmer);
if (debug)
@@ -33,3 +33,14 @@ Last-Update: Wed, 10 Oct 2018 12:49:34 +0200
// right extension
int len_right = traversal->traverse(kmer,right_traversal,strand);
+--- mapsembler2.orig/kissreads/src/kissReads.c
++++ mapsembler2/kissreads/src/kissReads.c
+@@ -93,7 +93,7 @@
+ fprintf (stderr, "\t -u file_name: write unread-coherent outputs. Default: standard output \n");
+ #ifndef INPUT_FROM_KISSPLICE
+ fprintf (stderr, "\t -n the input file (toCheck.fasta) is a kissnp output (incompatible with -I option) \n");
+- fprintf (stderr, "\t\t in this case: 1/ only the upper characters are considered (no mapping done on the extensions) and 2/ the central position (where the SNP occurs) is strictly mapped, no subsitution is authorized on this position.\n");
++ fprintf (stderr, "\t\t in this case: 1/ only the upper characters are considered (no mapping done on the extensions) and 2/ the central position (where the SNP occurs) is strictly mapped, no substitution is authorized on this position.\n");
+ fprintf (stderr, "\t -I the input file (toCheck.fasta) is an Intl output (incompatible with -n option) \n");
+ #endif // not INPUT_FROM_KISSPLICE
+ fprintf (stderr, "\t -i index_stride (int value). This is a heuristic for limiting the memory footprint. Instead of indexing each kmer of the sequences contained into the toCheck.fasta, kissreads indexes kmers occurring each \"index_stride\" position. Default = 1 (no heuristic)\n");
View it on GitLab: https://salsa.debian.org/med-team/mapsembler2/-/compare/94228d2f106c29f11b5b619cba9d7bae9573d971...df74cc12f18b06e63bc2832ba3a0fee34d71afa8
--
View it on GitLab: https://salsa.debian.org/med-team/mapsembler2/-/compare/94228d2f106c29f11b5b619cba9d7bae9573d971...df74cc12f18b06e63bc2832ba3a0fee34d71afa8
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