[med-svn] [Git][med-team/genometester][master] 6 commits: Remove binaries from upstream source, point watch file to Git HEAD
Andreas Tille
gitlab at salsa.debian.org
Sat Oct 6 11:13:25 BST 2018
Andreas Tille pushed to branch master at Debian Med / genometester
Commits:
b4577f5f by Andreas Tille at 2018-10-06T09:49:25Z
Remove binaries from upstream source, point watch file to Git HEAD
- - - - -
edc46387 by Andreas Tille at 2018-10-06T09:50:09Z
New upstream version 4.0+git20180508.a9c14a6+dfsg
- - - - -
659c6f9f by Andreas Tille at 2018-10-06T09:50:09Z
Update upstream source from tag 'upstream/4.0+git20180508.a9c14a6+dfsg'
Update to upstream version '4.0+git20180508.a9c14a6+dfsg'
with Debian dir 15af1db2fe9e407329e57dc7a8481fac041c04c3
- - - - -
d8dd447e by Andreas Tille at 2018-10-06T09:53:01Z
Update changelog
- - - - -
f1db1a30 by Andreas Tille at 2018-10-06T09:53:34Z
Standards-Version: 4.2.1
- - - - -
388474b1 by Andreas Tille at 2018-10-06T10:05:49Z
Upload to unstable
- - - - -
11 changed files:
- − bin/glistcompare
- − bin/glistmaker
- − bin/glistquery
- − bin/gmer_caller
- − bin/gmer_counter
- debian/changelog
- debian/control
- debian/copyright
- debian/watch
- src/Makefile
- src/gdistribution.c
Changes:
=====================================
bin/glistcompare deleted
=====================================
Binary files a/bin/glistcompare and /dev/null differ
=====================================
bin/glistmaker deleted
=====================================
Binary files a/bin/glistmaker and /dev/null differ
=====================================
bin/glistquery deleted
=====================================
Binary files a/bin/glistquery and /dev/null differ
=====================================
bin/gmer_caller deleted
=====================================
Binary files a/bin/gmer_caller and /dev/null differ
=====================================
bin/gmer_counter deleted
=====================================
Binary files a/bin/gmer_counter and /dev/null differ
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+genometester (4.0+git20180508.a9c14a6+dfsg-1) unstable; urgency=medium
+
+ * Remove binaries from upstream source
+ * Use git mode in watch file since gdistribution is needed by some
+ dependencies
+ * Standards-Version: 4.2.1
+
+ -- Andreas Tille <tille at debian.org> Sat, 06 Oct 2018 12:04:26 +0200
+
genometester (4.0-1) unstable; urgency=medium
* Initial release (Closes: #900752)
=====================================
debian/control
=====================================
@@ -5,7 +5,7 @@ Uploaders: Liubov Chuprikova <chuprikovalv at gmail.com>,
Section: science
Priority: optional
Build-Depends: debhelper (>= 11~)
-Standards-Version: 4.1.4
+Standards-Version: 4.2.1
Vcs-Browser: https://salsa.debian.org/med-team/genometester
Vcs-Git: https://salsa.debian.org/med-team/genometester.git
Homepage: https://github.com/bioinfo-ut/GenomeTester4
=====================================
debian/copyright
=====================================
@@ -1,6 +1,7 @@
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: GenomeTester4
Source: https://github.com/bioinfo-ut/GenomeTester4/releases
+Files-Excluded: */bin
Files: *
Copyright: 2014-2016 University of Tartu
=====================================
debian/watch
=====================================
@@ -1,4 +1,6 @@
version=4
-opts="uversionmangle=s/_/./g" \
- https://github.com/bioinfo-ut/GenomeTester4/releases .*/archive/Version_(\d[_.\d]+)@ARCHIVE_EXT@
+opts="mode=git,pretty=4.0+git%cd.%h,repacksuffix=+dfsg,dversionmangle=auto,uversionmangle=s/_/./g,repack,compression=xz" \
+ https://github.com/bioinfo-ut/GenomeTester4.git HEAD
+
+# https://github.com/bioinfo-ut/GenomeTester4/releases .*/archive/Version_(\d[_.\d]+)@ARCHIVE_EXT@
=====================================
src/Makefile
=====================================
@@ -8,9 +8,9 @@ CXX = gcc
LISTMAKER_SOURCES = \
glistmaker.c \
common.c common.h \
+ fasta.c fasta.h \
wordtable.c wordtable.h \
wordmap.c wordmap.h \
- fasta.c fasta.h \
buffer.c buffer.h \
sequence.c sequence.h \
sequence-file.c sequence-file.h \
@@ -54,6 +54,18 @@ LISTCOMPARE_SOURCES = \
queue.c queue.h \
utils.c
+GDISTRIBUTION_SOURCES = \
+ gdistribution.c \
+ wordtable.c \
+ wordmap.c \
+ fasta.c \
+ buffer.c \
+ sequence.c \
+ sequence-file.c sequence-file.h \
+ common.c \
+ queue.c queue.h \
+ utils.c
+
GMER_COUNTER_SOURCES = \
gmer_counter.c \
index.c index.h \
@@ -134,6 +146,9 @@ glistquery: $(LISTQUERY_SOURCES)
glistcompare: $(LISTCOMPARE_SOURCES)
$(CXX) $(LISTCOMPARE_SOURCES) -o glistcompare $(LIBS) $(CXXFLAGS)
+gdistribution: $(GDISTRIBUTION_SOURCES)
+ $(CXX) $(GDISTRIBUTION_SOURCES) -o gdistribution $(LIBS) $(CXXFLAGS)
+
gmer_counter: $(GMER_COUNTER_SOURCES)
$(CXX) $(GMER_COUNTER_SOURCES) -o gmer_counter $(LIBS) $(CXXFLAGS) -Wall
=====================================
src/gdistribution.c
=====================================
@@ -40,7 +40,7 @@ typedef struct {
unsigned int count;
} Freq;
-static void get_distribution (wordmap *maps[2]);
+static void get_distribution (GT4WordMap *maps[2]);
static void
print_usage (FILE *ofs) {
@@ -51,7 +51,7 @@ int
main (int argc, const char *argv[])
{
const char *names[2];
- wordmap *maps[2];
+ GT4WordMap *maps[2];
Freq *freqs;
if (argc < 3) {
@@ -64,8 +64,8 @@ main (int argc, const char *argv[])
if (debug) fprintf (stderr, "%s %s\n", names[0], names[1]);
- maps[0] = wordmap_new (names[0], 1);
- maps[1] = wordmap_new (names[1], 1);
+ maps[0] = gt4_wordmap_new (names[0], 1);
+ maps[1] = gt4_wordmap_new (names[1], 1);
get_distribution (maps);
@@ -79,7 +79,7 @@ static int compare (const void *lhs, const void *rhs) {
}
static void
-get_distribution (wordmap *maps[2])
+get_distribution (GT4WordMap *maps[2])
{
unsigned long long size, i0, i1, fidx;
unsigned int j, count;
View it on GitLab: https://salsa.debian.org/med-team/genometester/compare/faa8320a5f353b53602519c9c7558d6f9a4e3993...388474b10f6bcfc0153a0b44a544ff8cad38846b
--
View it on GitLab: https://salsa.debian.org/med-team/genometester/compare/faa8320a5f353b53602519c9c7558d6f9a4e3993...388474b10f6bcfc0153a0b44a544ff8cad38846b
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