Merge pull request #17 from gtamazian/master

Show version in help messages

src/Makefile

@@ -2,7 +2,7 @@ CXX = g++
 CXXFLAGS = -std=c++0x -Wall -O2
 PREFIX ?= /usr/local/bin
 
-OBJ = seq.o search.o stats.o fileroutines.o readroutines.o
+OBJ = seq.o search.o stats.o fileroutines.o readroutines.o version.o
 
 all: rm_reads extract remove separate
 
@@ -21,6 +21,9 @@ search.o: search.h search.cpp
 stats.o: stats.h stats.cpp
 	$(CXX) -c $(CXXFLAGS) stats.cpp
 
+version.o: version.h version.cpp
+	$(CXX) -c $(CXXFLAGS) version.cpp
+
 rm_reads: rm_reads.cpp $(OBJ)
 	$(CXX) $(CXXFLAGS) -o rm_reads rm_reads.cpp $(OBJ)
 

src/cookiecutter

@@ -428,7 +428,8 @@ def cookiecutter():
     """
     parser = argparse.ArgumentParser(
         description='Cookiecutter: a kmer-based read filtration and '
-                    'extraction tool.')
+                    'extraction tool.',
+        version='1.0.0')
     subparsers = parser.add_subparsers(dest='command')
 
     parser.add_argument('-e', '--echo', action='store_true',

src/extract.cpp

@@ -14,6 +14,7 @@
 #include "search.h"
 #include "stats.h"
 #include "seq.h"
+#include "version.h"
 
 /*! \brief Read adapter patterns from an input stream
  *
@@ -144,6 +145,7 @@ void print_help()
 {
     std::cerr << "Usage:" << std::endl;
     std::cerr << "extract [-i raw_data.fastq | -1 raw_data1.fastq -2 raw_data2.fastq] -o output_dir --fragments fragments.dat" << std::endl;
+	show_version();
 }
 
 /*! \brief The main function of the **extract** tool. */

src/remove.cpp

@@ -15,6 +15,7 @@
 #include "search.h"
 #include "stats.h"
 #include "seq.h"
+#include "version.h"
 
 /*! \brief Read adapter patterns from an input stream
  *
@@ -123,6 +124,7 @@ void print_help()
 {
     std::cerr << "Usage:" << std::endl;
     std::cerr << "remove [-i raw_data.fastq | -1 raw_data1.fastq -2 raw_data2.fastq] -o output_dir --fragments fragments.dat" << std::endl;
+	show_version();
 }
 
 /*! \brief The main function of the **remove** tool. */

src/rm_reads.cpp

@@ -15,6 +15,7 @@
 #include "search.h"
 #include "stats.h"
 #include "seq.h"
+#include "version.h"
 
 /*! \brief Read adapter patterns from an input stream
  *
@@ -145,6 +146,7 @@ void print_help()
 {
     std::cerr << "Usage:" << std::endl;
     std::cerr << "rm_reads [-i raw_data.fastq | -1 raw_data1.fastq -2 raw_data2.fastq] -o output_dir --polyG 13 --length 50 --fragments fragments.dat --dust_cutoff cutoff --dust_k k" << std::endl;
+	show_version();
 }
 
 /*! \brief The main function of the **rm_reads** tool. */

src/separate.cpp

@@ -15,6 +15,7 @@
 #include "search.h"
 #include "stats.h"
 #include "seq.h"
+#include "version.h"
 
 /*! \brief Read adapter patterns from an input stream
  *
@@ -140,6 +141,7 @@ void print_help()
 {
     std::cerr << "Usage:" << std::endl;
     std::cerr << "separate [-i raw_data.fastq | -1 raw_data1.fastq -2 raw_data2.fastq] -o output_dir --fragments fragments.dat" << std::endl;
+	show_version();
 }
 
 /*! \brief The main function of the **rm_reads** tool. */

src/version.cpp

@@ -0,0 +1,7 @@
+#include "version.h"
+
+void show_version()
+{
+	std::cerr << "Version: " << version << std::endl;
+}
+

src/version.h

@@ -0,0 +1,7 @@
+#include <iostream>
+#include <string>
+
+static const std::string version = "1.0.0";
+
+void show_version();
+