debian/changelog

+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@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@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

 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

 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;