added version to subcommands

src/annotateBed/Makefile

@@ -9,7 +9,8 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
 			-I$(UTILITIES_DIR)/lineFileUtilities/ \
 			-I$(UTILITIES_DIR)/BamTools/ \
 			-I$(UTILITIES_DIR)/gzstream/ \
-			-I$(UTILITIES_DIR)/fileType/
+			-I$(UTILITIES_DIR)/fileType/ \
+			-I$(UTILITIES_DIR)/version/
 
 # ----------------------------------
 # define our source and object files

src/annotateBed/annotateMain.cpp

@@ -10,6 +10,7 @@
   Licenced under the GNU General Public License 2.0 license.
 ******************************************************************************/
 #include "annotateBed.h"
+#include "version.h"
 
 using namespace std;
 
@@ -140,6 +141,7 @@ int annotate_main(int argc, char* argv[]) {
 void annotate_help(void) {
 
     cerr << "\nTool:    bedtools annotate (aka annotateBed)" << endl;
+    cerr << "Version: " << VERSION << "\n";
     cerr << "Summary: Annotates the depth & breadth of coverage of features from mult. files" << endl;
     cerr << "\t on the intervals in -i." << endl << endl;
 

src/bamToBed/Makefile

@@ -10,7 +10,8 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
            -I$(UTILITIES_DIR)/lineFileUtilities/ \
            -I$(UTILITIES_DIR)/fileType/ \
            -I$(UTILITIES_DIR)/BamTools/include \
-		   -I$(UTILITIES_DIR)/BamTools-Ancillary
+		   -I$(UTILITIES_DIR)/BamTools-Ancillary \
+		   -I$(UTILITIES_DIR)/version/
 
 
 # ----------------------------------

src/bamToBed/bamToBed.cpp

@@ -13,6 +13,7 @@
 #include "api/BamAux.h"
 #include "BamAncillary.h"
 #include "bedFile.h"
+#include "version.h"
 using namespace BamTools;
 
 #include <vector>
@@ -186,7 +187,7 @@ int bamtobed_main(int argc, char* argv[]) {
 void bamtobed_help(void) {
     
     cerr << "\nTool:    bedtools bamtobed (aka bamToBed)" << endl;
-
+    cerr << "Version: " << VERSION << "\n";
     cerr << "Summary: Converts BAM alignments to BED6 or BEDPE format." << endl << endl;
 
     cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -i <bam> " << endl << endl;

src/bed12ToBed6/Makefile

@@ -8,7 +8,8 @@ BIN_DIR = ../../bin/
 INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
            -I$(UTILITIES_DIR)/lineFileUtilities/ \
            -I$(UTILITIES_DIR)/gzstream/ \
-           -I$(UTILITIES_DIR)/fileType/
+           -I$(UTILITIES_DIR)/fileType/ \
+           -I$(UTILITIES_DIR)/version/
 
 # ----------------------------------
 # define our source and object files

src/bed12ToBed6/bed12ToBed6.cpp

@@ -11,7 +11,7 @@
 ******************************************************************************/
 #include "lineFileUtilities.h"
 #include "bedFile.h"
-
+#include "version.h"
 #include <vector>
 #include <iostream>
 #include <fstream>
@@ -96,7 +96,7 @@ int bed12tobed6_main(int argc, char* argv[]) {
 void bed12tobed6_help(void) {
 
     cerr << "\nTool:    bedtools bed12tobed6 (aka bed12ToBed6)" << endl;
-    
+    cerr << "Version: " << VERSION << "\n";
     cerr << "Summary: Splits BED12 features into discrete BED6 features." << endl << endl;
 
     cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -i <bed12>" << endl << endl;

src/bedToBam/Makefile

@@ -12,7 +12,8 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
            -I$(UTILITIES_DIR)/lineFileUtilities/ \
            -I$(UTILITIES_DIR)/fileType/ \
            -I$(UTILITIES_DIR)/BamTools/include \
-		   -I$(UTILITIES_DIR)/BamTools-Ancillary
+		   -I$(UTILITIES_DIR)/BamTools-Ancillary \
+		   -I$(UTILITIES_DIR)/version/
 
 # ----------------------------------
 # define our source and object files

src/bedToBam/bedToBam.cpp

@@ -140,7 +140,7 @@ int bedtobam_main(int argc, char* argv[]) {
 void bedtobam_help(void) {
     
     cerr << "\nTool:    bedtools bedtobam (aka bedToBam)" << endl;
-
+    cerr << "Version: " << VERSION << "\n";
     cerr << "Summary: Converts feature records to BAM format." << endl << endl;
 
     cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -i <bed/gff/vcf> -g <genome>" << endl << endl;

src/bedToIgv/Makefile

@@ -10,7 +10,8 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
            -I$(UTILITIES_DIR)/lineFileUtilities/ \
            -I$(UTILITIES_DIR)/gzstream/ \
            -I$(UTILITIES_DIR)/fileType/ \
-           -I$(UTILITIES_DIR)/BamTools/include
+           -I$(UTILITIES_DIR)/BamTools/include \
+           -I$(UTILITIES_DIR)/version/
 
 # ----------------------------------
 # define our source and object files

src/bedToIgv/bedToIgv.cpp

@@ -12,6 +12,7 @@
 #include "lineFileUtilities.h"
 #include "bedFile.h"
 #include "genomeFile.h"
+#include "version.h"
 
 #include <vector>
 #include <iostream>
@@ -147,7 +148,7 @@ int bedtoigv_main(int argc, char* argv[]) {
 void bedtoigv_help(void) {
 
     cerr << "\nTool:    bedtools igv (aka bedToIgv)" << endl;
-
+    cerr << "Version: " << VERSION << "\n";
     cerr << "Summary: Creates a batch script to create IGV images " << endl;
     cerr << "         at each interval defined in a BED/GFF/VCF file." << endl << endl;
 

src/bedpeToBam/Makefile

@@ -13,7 +13,8 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
            -I$(UTILITIES_DIR)/lineFileUtilities/ \
            -I$(UTILITIES_DIR)/fileType/ \
            -I$(UTILITIES_DIR)/BamTools/include \
-		   -I$(UTILITIES_DIR)/BamTools-Ancillary
+		   -I$(UTILITIES_DIR)/BamTools-Ancillary \
+		   -I$(UTILITIES_DIR)/version/
 
 # ----------------------------------
 # define our source and object files

src/bedpeToBam/bedpeToBam.cpp

@@ -138,7 +138,7 @@ int bedpetobam_main(int argc, char* argv[]) {
 void bedpetobam_help(void) {
     
     cerr << "\nTool:    bedtools bedpetobam (aka bedpeToBam)" << endl;
-
+    cerr << "Version: " << VERSION << "\n";
     cerr << "Summary: Converts feature records to BAM format." << endl << endl;
 
     cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -i <bed/gff/vcf> -g <genome>" << endl << endl;

src/closestBed/Makefile

@@ -8,7 +8,8 @@ BIN_DIR = ../../bin/
 INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
            -I$(UTILITIES_DIR)/lineFileUtilities/ \
            -I$(UTILITIES_DIR)/gzstream/ \
-           -I$(UTILITIES_DIR)/fileType/
+           -I$(UTILITIES_DIR)/fileType/ \
+           -I$(UTILITIES_DIR)/version/
 # ----------------------------------
 # define our source and object files
 # ----------------------------------

src/closestBed/closestMain.cpp

@@ -10,6 +10,7 @@
   Licenced under the GNU General Public License 2.0 license.
 ******************************************************************************/
 #include "closestBed.h"
+#include "version.h"
 
 using namespace std;
 
@@ -153,7 +154,7 @@ int closest_main(int argc, char* argv[]) {
 void closest_help(void) {
     
     cerr << "\nTool:    bedtools closest (aka closestBed)" << endl;
-
+    cerr << "Version: " << VERSION << "\n";
     cerr << "Summary: For each feature in A, finds the closest " << endl;
     cerr << "\t feature (upstream or downstream) in B." << endl << endl;
 

src/complementBed/Makefile

@@ -10,7 +10,8 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
            -I$(UTILITIES_DIR)/lineFileUtilities/ \
            -I$(UTILITIES_DIR)/gzstream/ \
            -I$(UTILITIES_DIR)/fileType/ \
-           -I$(UTILITIES_DIR)/BamTools/include
+           -I$(UTILITIES_DIR)/BamTools/include \
+           -I$(UTILITIES_DIR)/version/
 
 # ----------------------------------
 # define our source and object files

src/complementBed/complementMain.cpp

@@ -10,6 +10,7 @@
   Licenced under the GNU General Public License 2.0 license.
 ******************************************************************************/
 #include "complementBed.h"
+#include "version.h"
 
 using namespace std;
 
@@ -88,7 +89,7 @@ int complement_main(int argc, char* argv[]) {
 void complement_help(void) {
 
     cerr << "\nTool:    bedtools complement (aka complementBed)" << endl;
-    
+    cerr << "Version: " << VERSION << "\n";    
     cerr << "Summary: Returns the base pair complement of a feature file." << endl << endl;
 
     cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -i <bed/gff/vcf> -g <genome>" << endl << endl;

src/coverageBed/Makefile

@@ -11,7 +11,8 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
            -I$(UTILITIES_DIR)/lineFileUtilities/ \
            -I$(UTILITIES_DIR)/fileType/ \
            -I$(UTILITIES_DIR)/BamTools/include \
-		   -I$(UTILITIES_DIR)/BamTools-Ancillary
+		   -I$(UTILITIES_DIR)/BamTools-Ancillary \
+		   -I$(UTILITIES_DIR)/version/
 # ----------------------------------
 # define our source and object files
 # ----------------------------------

src/coverageBed/coverageMain.cpp

@@ -10,6 +10,7 @@
   Licenced under the GNU General Public License 2.0 license.
 ******************************************************************************/
 #include "coverageBed.h"
+#include "version.h"
 
 using namespace std;
 
@@ -132,7 +133,7 @@ int coverage_main(int argc, char* argv[]) {
 void coverage_help(void) {
 
     cerr << "\nTool:    bedtools coverage (aka coverageBed)" << endl;
-    
+    cerr << "Version: " << VERSION << "\n";    
     cerr << "Summary: Returns the depth and breadth of coverage of features from A" << endl;
     cerr << "\t on the intervals in B." << endl << endl;
 

src/fastaFromBed/Makefile

@@ -12,6 +12,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
            -I$(UTILITIES_DIR)/sequenceUtilities/ \
            -I$(UTILITIES_DIR)/fileType/ \
            -I$(UTILITIES_DIR)/Fasta/ \
+           -I$(UTILITIES_DIR)/version/
 
 # ----------------------------------
 # define our source and object files

src/fastaFromBed/fastaFromBedMain.cpp

@@ -10,6 +10,7 @@
   Licenced under the GNU General Public License 2.0 license.
 ******************************************************************************/
 #include "fastaFromBed.h"
+#include "version.h"
 
 using namespace std;
 
@@ -116,7 +117,7 @@ int fastafrombed_main(int argc, char* argv[]) {
 void fastafrombed_help(void) {
     
     cerr << "\nTool:    bedtools getfasta (aka fastaFromBed)" << endl;
-
+    cerr << "Version: " << VERSION << "\n";
     cerr << "Summary: Extract DNA sequences into a fasta file based on feature coordinates." << endl << endl;
 
     cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -fi <fasta> -bed <bed/gff/vcf> -fo <fasta> " << endl << endl;