minor changes

sequencing · Aug 13, 2015 · 177318b · 177318b
1 parent 8bb986b
commit 177318b
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Showing 8 changed files with 29 additions and 21 deletions.
diff --git a/Changes b/Changes
@@ -1,3 +1,7 @@
+2015.08.13
+*makefile/versioning tweaks
+*added some more examples
+
 2015.05.26
 *minor bugfix concerning --justmp and external adapters
 

diff --git a/Makefile b/Makefile
@@ -4,22 +4,31 @@ ifndef BOOST_ROOT
     $(error BOOST_ROOT is undefined.  Point BOOST_ROOT at your boost installation ie. BOOST_ROOT/lib and BOOST_ROOT/include should exist)
 endif
 
-LFLAGS = -L$(BOOST_ROOT)/lib -lz -lboost_iostreams  -lboost_program_options
+
 CFLAGS = -O3  -I$(BOOST_ROOT)/include
+LFLAGS=  $(BOOST_ROOT)/lib/libboost_iostreams.a $(BOOST_ROOT)/lib/libboost_program_options.a -lz
+
+all: mergeReads nxtrim
 
 
-static: LFLAGS=  $(BOOST_ROOT)/lib/libboost_iostreams.a $(BOOST_ROOT)/lib/libboost_program_options.a -lz
-static: all
 
 debug: CFLAGS = -Wall -g -I$(BOOST_ROOT)/include
 debug: all
 
-all: mergeReads nxtrim 
+GIT_HASH := $(shell git describe --abbrev=4 --always )
+
+VERSION = v0.3.2-alpha
+GIT_VERSION =
+ifneq "$(wildcard .git)" ""
+GIT_VERSION = -$(shell git describe --always)
+endif
+version.h:
+	echo '#define VERSION "$(VERSION)$(GIT_VERSION)"' > $@
+
+
 test: test.cpp fastqlib.o utilityfunc.o matepair.o
-	$(CC) $(CFLAGS) test.cpp fastqlib.o utilityfunc.o matepair.o -o test   $(LFLAGS) 
-githash.h: 
-	git log -1 --format="#define HASH \"%h\"" > githash.h	
-nxtrim: nxtrim.cpp fastqlib.o utilityfunc.o matepair.o fastqlib.o githash.h version.h
+	$(CC) $(CFLAGS) test.cpp fastqlib.o utilityfunc.o matepair.o -o test   $(LFLAGS)
+nxtrim: nxtrim.cpp fastqlib.o utilityfunc.o matepair.o fastqlib.o version.h
 	$(CC) $(CFLAGS) nxtrim.cpp fastqlib.o utilityfunc.o matepair.o -o nxtrim  $(LFLAGS)
 mergeReads: mergeReads.cpp fastqlib.o utilityfunc.o fastqlib.o githash.h version.h
 	$(CC) $(CFLAGS)  mergeReads.cpp fastqlib.o utilityfunc.o -o mergeReads   $(LFLAGS)
@@ -30,7 +39,5 @@ fastqlib.o: fastqlib.cpp fastqlib.h utilityfunc.h
 utilityfunc.o:  utilityfunc.cpp utilityfunc.h
 	$(CC) $(CFLAGS) -c utilityfunc.cpp 
 clean:
-	rm *.o
-	rm nxtrim
-	rm test
-	rm mergeReads
+	rm *.o nxtrim test mergeReads version.h
+
diff --git a/example/issue12_R1.fastq.gz b/example/issue12_R1.fastq.gz
diff --git a/example/issue12_R2.fastq.gz b/example/issue12_R2.fastq.gz
diff --git a/fastqlib.cpp b/fastqlib.cpp
@@ -124,14 +124,13 @@ fqread fqread::window(int a) {
   return(fqread(h,s.substr(a),l3,q.substr(a)));
 }
 
-int fqread::print() {
+void fqread::print() {
   if(l>0) {
     cout << h << endl;
     cout << s << endl;
     cout <<l3 << endl;
     cout << q << endl;
   }
-  return(0);
 }
 
 
@@ -207,7 +206,7 @@ readPair pairReader::next() {
   return( readPair(f1->next(),f2->next()));
 }
 
-int readPair::print() {
+void readPair::print() {
   r1.print();
   r2.print();
 }

diff --git a/fastqlib.h b/fastqlib.h
@@ -16,7 +16,7 @@ class fqread {
   fqread window(int a,int b);
   fqread window(int a);
   fqread rc();
-  int print();
+  void print();
   int clear();
 };
 
@@ -26,7 +26,7 @@ class readPair {
   readPair(fqread read1,fqread read2);
   int rc();
   int set(fqread read1, fqread read2);
-  int print();
+  void print();
   fqread r1,r2;
   int l;
   bool filtered;

diff --git a/nxtrim.cpp b/nxtrim.cpp
@@ -1,5 +1,4 @@
 #include "version.h"
-#include "githash.h"
 #include "matepair.h"
 #include "fastqlib.h"
 #include <boost/program_options.hpp>
@@ -14,7 +13,7 @@ string percent(int num,int den) {
 }
 
 int checkParameters(int argc,char **argv,po::variables_map & vm) {
-    cerr << "\nNxTrim "<<VERSION<<" "<<HASH<<endl<<endl;
+    cerr << "\nNxTrim "<<VERSION<<endl<<endl;
 
   po::options_description desc("Allowed options");
   try{

diff --git a/version.h b/version.h
@@ -1,2 +1 @@
-#define VERSION "v0.3.2-alpha"
-
+#define VERSION "v0.3.2-alpha-8bb986b"
Original file line number	Diff line number	Diff line change
		@@ -1,2 +1 @@
		#define VERSION "v0.3.2-alpha"

		#define VERSION "v0.3.2-alpha-8bb986b"