Commit f8d62267 authored by Aaron's avatar Aaron
Browse files

added version to subcommands

parent 53feac20
......@@ -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$(UTILITIES_DIR)/version/
# ----------------------------------
# define our source and object files
......
......@@ -10,6 +10,7 @@
Licenced under the GNU General Public License 2.0 license.
******************************************************************************/
#include "annotateBed.h"
#include "version.h"
using namespace std;
......@@ -140,6 +141,7 @@ int annotate_main(int argc, char* argv[]) {
void annotate_help(void) {
cerr << "\nTool: bedtools annotate (aka annotateBed)" << endl;
cerr << "Version: " << VERSION << "\n";
cerr << "Summary: Annotates the depth & breadth of coverage of features from mult. files" << endl;
cerr << "\t on the intervals in -i." << endl << endl;
......
......@@ -10,7 +10,8 @@ INCLUDES = -I$(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/
# ----------------------------------
......
......@@ -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;
......
......@@ -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
......
......@@ -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;
......
......@@ -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$(UTILITIES_DIR)/version/
# ----------------------------------
# define our source and object files
......
......@@ -140,7 +140,7 @@ int bedtobam_main(int argc, char* argv[]) {
void bedtobam_help(void) {
cerr << "\nTool: bedtools bedtobam (aka bedToBam)" << endl;
cerr << "Version: " << VERSION << "\n";
cerr << "Summary: Converts feature records to BAM format." << endl << endl;
cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <bed/gff/vcf> -g <genome>" << endl << endl;
......
......@@ -10,7 +10,8 @@ INCLUDES = -I$(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
......
......@@ -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;
......
......@@ -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$(UTILITIES_DIR)/version/
# ----------------------------------
# define our source and object files
......
......@@ -138,7 +138,7 @@ int bedpetobam_main(int argc, char* argv[]) {
void bedpetobam_help(void) {
cerr << "\nTool: bedtools bedpetobam (aka bedpeToBam)" << endl;
cerr << "Version: " << VERSION << "\n";
cerr << "Summary: Converts feature records to BAM format." << endl << endl;
cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <bed/gff/vcf> -g <genome>" << endl << endl;
......
......@@ -8,7 +8,8 @@ BIN_DIR = ../../bin/
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
-I$(UTILITIES_DIR)/lineFileUtilities/ \
-I$(UTILITIES_DIR)/gzstream/ \
-I$(UTILITIES_DIR)/fileType/
-I$(UTILITIES_DIR)/fileType/ \
-I$(UTILITIES_DIR)/version/
# ----------------------------------
# define our source and object files
# ----------------------------------
......
......@@ -10,6 +10,7 @@
Licenced under the GNU General Public License 2.0 license.
******************************************************************************/
#include "closestBed.h"
#include "version.h"
using namespace std;
......@@ -153,7 +154,7 @@ int closest_main(int argc, char* argv[]) {
void closest_help(void) {
cerr << "\nTool: bedtools closest (aka closestBed)" << endl;
cerr << "Version: " << VERSION << "\n";
cerr << "Summary: For each feature in A, finds the closest " << endl;
cerr << "\t feature (upstream or downstream) in B." << endl << endl;
......
......@@ -10,7 +10,8 @@ INCLUDES = -I$(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
......
......@@ -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;
......
......@@ -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$(UTILITIES_DIR)/version/
# ----------------------------------
# define our source and object files
# ----------------------------------
......
......@@ -10,6 +10,7 @@
Licenced under the GNU General Public License 2.0 license.
******************************************************************************/
#include "coverageBed.h"
#include "version.h"
using namespace std;
......@@ -132,7 +133,7 @@ int coverage_main(int argc, char* argv[]) {
void coverage_help(void) {
cerr << "\nTool: bedtools coverage (aka coverageBed)" << endl;
cerr << "Version: " << VERSION << "\n";
cerr << "Summary: Returns the depth and breadth of coverage of features from A" << endl;
cerr << "\t on the intervals in B." << endl << endl;
......
......@@ -12,6 +12,7 @@ INCLUDES = -I$(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
......
......@@ -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;
......
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