➖ remove gengetopt dependency

Author: nrizzo

Makefile

@@ -2,3 +2,4 @@
 prerequisites:
 	make --directory=tools/efg-locate
 	make --directory=tools/ChainX-block-graph
+	make --directory=tools/efg-gaf-splitter

tools/ChainX-block-graph/Makefile

@@ -9,16 +9,23 @@ chainx-block-graph : chainx-block-graph.cpp chainx-block-graph.hpp chaining.hpp
 	chainx-block-graph.cpp command-line-parsing/cmdline.c \
 	-o chainx-block-graph
 
-command-line-parsing/cmdline%c command-line-parsing/cmdline%h : command-line-parsing/config.ggo
-	gengetopt \
-		--input=./command-line-parsing/config.ggo \
-		--output-dir=./command-line-parsing/ \
-		--unnamed-opts
+# uncomment for development
+#command-line-parsing/cmdline%c command-line-parsing/cmdline%h : command-line-parsing/config.ggo
+#	gengetopt \
+#		--input=./command-line-parsing/config.ggo \
+#		--output-dir=./command-line-parsing/ \
+#		--unnamed-opts
 
 test : chainx-block-graph test/test.sh
 	test/test.sh
 
-.PHONY : clean all test
+.PHONY : clean all test cleanall
 
+#clean :
+#	rm -Rf command-line-parsing/cmdline.c command-line-parsing/cmdline.h test/output*
+#cleanall :
+#	rm -Rf chainx-block-graph command-line-parsing/cmdline.c command-line-parsing/cmdline.h test/output*
 clean :
-	rm -Rf chainx-block-graph command-line-parsing/cmdline.{c,h} test/output*
+	rm -Rf test/output*
+cleanall :
+	rm -Rf chainx-block-graph test/output*

tools/ChainX-block-graph/README.md

@@ -2,7 +2,6 @@
 Program to perform co-linear chaining on the Elastic Degenerate String relaxation of Elastic Founder Graphs.
 
 ## todo
- - remove gengetopt dependency
  - always collect statistics
  - docs
  - more tests trying complex chains

tools/efg-gaf-splitter/Makefile

@@ -8,15 +8,18 @@ efg-gaf-splitter : efg-gaf-splitter.cpp efg.hpp command-line-parsing/cmdline.h c
 	efg-gaf-splitter.cpp command-line-parsing/cmdline.c \
 	-o efg-gaf-splitter
 
-command-line-parsing/cmdline%c command-line-parsing/cmdline%h : command-line-parsing/config.ggo
-	gengetopt \
-		--input=./command-line-parsing/config.ggo \
-		--output-dir=./command-line-parsing/ \
-		--unnamed-opts
+# uncomment for development
+#command-line-parsing/cmdline%c command-line-parsing/cmdline%h : command-line-parsing/config.ggo
+#	gengetopt \
+#		--input=./command-line-parsing/config.ggo \
+#		--output-dir=./command-line-parsing/ \
+#		--unnamed-opts
 
-.PHONY : clean all
+.PHONY : clean all cleanall
 
-clean :
-	rm -Rf command-line-parsing/cmdline.{c,h}
+#clean :
+#	rm -Rf command-line-parsing/cmdline.c command-line-parsing/cmdline.h
+#cleanall :
+#	rm -Rf efg-gaf-splitter command-line-parsing/cmdline.c command-line-parsing/cmdline.h
 cleanall :
-	rm -Rf efg-gaf-splitter command-line-parsing/cmdline.{c,h}
+	rm -Rf efg-gaf-splitter

tools/efg-locate/Makefile

@@ -9,15 +9,18 @@ efg-locate : efg-locate.cpp efg.hpp algo.cpp command-line-parsing/cmdline.h comm
 	efg-locate.cpp command-line-parsing/cmdline.c \
 	-o efg-locate
 
-command-line-parsing/cmdline%c command-line-parsing/cmdline%h : command-line-parsing/config.ggo
-	gengetopt \
-		--input=./command-line-parsing/config.ggo \
-		--output-dir=./command-line-parsing/ \
-		--unnamed-opts
+# uncomment for development
+#command-line-parsing/cmdline%c command-line-parsing/cmdline%h : command-line-parsing/config.ggo
+#	gengetopt \
+#		--input=./command-line-parsing/config.ggo \
+#		--output-dir=./command-line-parsing/ \
+#		--unnamed-opts
 
-.PHONY : clean all
+.PHONY : clean all cleanall
 
-clean :
-	rm -Rf command-line-parsing/cmdline.{c,h}
+#clean :
+#	rm -Rf command-line-parsing/cmdline.c command-line-parsing/cmdline.h
+#cleanall :
+#	rm -Rf efg-locate command-line-parsing/cmdline.c command-line-parsing/cmdline.h
 cleanall :
-	rm -Rf efg-locate command-line-parsing/cmdline.{c,h}
+	rm -Rf efg-locate

tools/efg-locate/README.md

@@ -2,6 +2,5 @@
 Perform exact or approximate pattern matching on Elastic Founder Graphs.
 
 ## TODO
- - remove gengetopt dependency
  - documentation
  - more tests