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 <[email protected]> Sun, 21 Feb 2021 15:25:45 +0100 + -- Étienne Mollier <[email protected]> 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 <[email protected]> Uploaders: Olivier Sallou <[email protected]>, Andreas Tille <[email protected]>, - Étienne Mollier <[email protected]> + Étienne Mollier <[email protected]> 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 <[email protected]> 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 You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
