Changed the usage banner on all programs to be less showy

src/complementBed/complementMain.cpp

@@ -79,14 +79,11 @@ int main(int argc, char* argv[]) {
 
 void ShowHelp(void) {
 	
-	cerr << "=======================================================" << endl;
-	cerr << PROGRAM_NAME << " v" << VERSION << endl ;
-	cerr << "Aaron Quinlan, Ph.D." << endl;
-	cerr << "aaronquinlan@gmail.com" << endl ;
-	cerr << "Hall Laboratory" << endl;
-	cerr << "Biochemistry and Molecular Genetics" << endl;
-	cerr << "University of Virginia" << endl; 
-	cerr << "=======================================================" << endl << endl;
+	cerr << "===============================================" << endl;
+	cerr << " " <<PROGRAM_NAME << " v" << VERSION << endl ;
+	cerr << " Aaron Quinlan, Ph.D. (aaronquinlan@gmail.com)  " << endl ;
+	cerr << " Hall Laboratory, University of Virginia" << endl;
+	cerr << "===============================================" << endl << endl;
 	cerr << "Description: Returns the base pair complement of a BED file." << endl << endl;
 	cerr << "***NOTE: Only BED3 - BED6 formats allowed.***"<< endl << endl;
 

src/coverageBed/coverageMain.cpp

@@ -80,14 +80,11 @@ int main(int argc, char* argv[]) {
 
 void ShowHelp(void) {
 
-	cerr << "=======================================================" << endl;
-	cerr << PROGRAM_NAME << " v" << VERSION << endl ;
-	cerr << "Aaron Quinlan, Ph.D." << endl;
-	cerr << "aaronquinlan@gmail.com" << endl ;
-	cerr << "Hall Laboratory" << endl;
-	cerr << "Biochemistry and Molecular Genetics" << endl;
-	cerr << "University of Virginia" << endl; 
-	cerr << "=======================================================" << endl << endl;
+	cerr << "===============================================" << endl;
+	cerr << " " <<PROGRAM_NAME << " v" << VERSION << endl ;
+	cerr << " Aaron Quinlan, Ph.D. (aaronquinlan@gmail.com)  " << endl ;
+	cerr << " Hall Laboratory, University of Virginia" << endl;
+	cerr << "===============================================" << endl << endl;
 	//cerr << "Description: Reportoverlaps between a.bed and b.bed." << endl << endl;
 	cerr << "***NOTE: Only BED3 - BED6 formats allowed.***"<< endl << endl;
 

src/fastaFromBed/fastaFromBedMain.cpp

@@ -94,14 +94,11 @@ int main(int argc, char* argv[]) {
 
 void ShowHelp(void) {
 	
-	cerr << "=======================================================" << endl;
-	cerr << PROGRAM_NAME << " v" << VERSION << endl << endl;
-	cerr << "Aaron Quinlan, Ph.D." << endl;
-	cerr << "aaronquinlan@gmail.com" << endl << endl;
-	cerr << "Hall Laboratory" << endl;
-	cerr << "Biochemistry and Molecular Genetics" << endl;
-	cerr << "University of Virginia" << endl; 
-	cerr << "=======================================================" << endl << endl;
+	cerr << "===============================================" << endl;
+	cerr << " " <<PROGRAM_NAME << " v" << VERSION << endl ;
+	cerr << " Aaron Quinlan, Ph.D. (aaronquinlan@gmail.com)  " << endl ;
+	cerr << " Hall Laboratory, University of Virginia" << endl;
+	cerr << "===============================================" << endl << endl;
 	cerr << "Description: Extract DNA sequences into a fasta file based on BED coordinates." << endl << endl;
 
 	cerr << "Usage: " << PROGRAM_NAME << " -db <fasta db file> -bed <bed coordinates file> -fo <output fasta file w/ requested DNA>" << endl << endl;

src/genomeCoverageBed/genomeCoverageMain.cpp

@@ -97,14 +97,11 @@ int main(int argc, char* argv[]) {
 
 void ShowHelp(void) {
 	
-	cerr << "=======================================================" << endl;
-	cerr << PROGRAM_NAME << " v" << VERSION << endl ;
-	cerr << "Aaron Quinlan, Ph.D." << endl;
-	cerr << "aaronquinlan@gmail.com" << endl ;
-	cerr << "Hall Laboratory" << endl;
-	cerr << "Biochemistry and Molecular Genetics" << endl;
-	cerr << "University of Virginia" << endl; 
-	cerr << "=======================================================" << endl << endl;
+	cerr << "===============================================" << endl;
+	cerr << " " <<PROGRAM_NAME << " v" << VERSION << endl ;
+	cerr << " Aaron Quinlan, Ph.D. (aaronquinlan@gmail.com)  " << endl ;
+	cerr << " Hall Laboratory, University of Virginia" << endl;
+	cerr << "===============================================" << endl << endl;
 	cerr << "Description: Compute the coverage of a BED (-i) file on genome (-g) file." << endl << endl;
 	cerr << "***NOTE: Only BED3 - BED6 formats allowed.***"<< endl << endl;
 

src/intersectBed/intersectMain.cpp

@@ -130,14 +130,11 @@ int main(int argc, char* argv[]) {
 
 void ShowHelp(void) {
 
-	cerr << "=======================================================" << endl;
-	cerr << PROGRAM_NAME << " v" << VERSION << endl ;
-	cerr << "Aaron Quinlan, Ph.D." << endl;
-	cerr << "aaronquinlan@gmail.com" << endl ;
-	cerr << "Hall Laboratory" << endl;
-	cerr << "Biochemistry and Molecular Genetics" << endl;
-	cerr << "University of Virginia" << endl; 
-	cerr << "=======================================================" << endl << endl;
+	cerr << "===============================================" << endl;
+	cerr << " " <<PROGRAM_NAME << " v" << VERSION << endl ;
+	cerr << " Aaron Quinlan, Ph.D. (aaronquinlan@gmail.com)  " << endl ;
+	cerr << " Hall Laboratory, University of Virginia" << endl;
+	cerr << "===============================================" << endl << endl;
 	cerr << "Description: Report overlaps between a.bed and b.bed." << endl << endl;
 	cerr << "***NOTE: Only BED3 - BED6 formats allowed.***"<< endl << endl;
 
@@ -146,7 +143,6 @@ void ShowHelp(void) {
 	cerr << "OPTIONS: " << endl;
 	cerr << "\t" << "-u\t\t\t"            	<< "Write ORIGINAL a.bed entry ONCE if ANY overlap bed." << endl << "\t\t\t\tIn other words, ignore multiple overlaps." << endl << endl;
 	cerr << "\t" << "-v \t\t\t"             << "Only report those entries in A that have NO OVERLAP in B." << endl << "\t\t\t\tSimilar to grep -v." << endl << endl;
-	cerr << "\t" << "-s (100000)\t\t"	    << "Slop added before and after each entry in A" << endl << "\t\t\t\tUseful for finding overlaps within N bases upstream and downstream." << endl << endl;	
 	cerr << "\t" << "-f (e.g. 0.05)\t\t"	<< "Minimum overlap req'd as fraction of a.bed." << endl << "\t\t\t\tDefault is 1E-9 (effectively 1bp)." << endl << endl;
 	cerr << "\t" << "-c \t\t\t"				<< "For each entry in A, report the number of hits in B while restricting to -f." << endl << "\t\t\t\tReports 0 for A entries that have no overlap with B." << endl << endl;
 	cerr << "\t" << "-wa \t\t\t"			<< "Write the original entry in A for each overlap." << endl << endl;

src/mergeBed/mergeMain.cpp

@@ -86,14 +86,11 @@ int main(int argc, char* argv[]) {
 
 void ShowHelp(void) {
 	
-	cerr << "=======================================================" << endl;
-	cerr << PROGRAM_NAME << " v" << VERSION << endl ;
-	cerr << "Aaron Quinlan, Ph.D." << endl;
-	cerr << "aaronquinlan@gmail.com" << endl ;
-	cerr << "Hall Laboratory" << endl;
-	cerr << "Biochemistry and Molecular Genetics" << endl;
-	cerr << "University of Virginia" << endl; 
-	cerr << "=======================================================" << endl << endl;
+	cerr << "===============================================" << endl;
+	cerr << " " <<PROGRAM_NAME << " v" << VERSION << endl ;
+	cerr << " Aaron Quinlan, Ph.D. (aaronquinlan@gmail.com)  " << endl ;
+	cerr << " Hall Laboratory, University of Virginia" << endl;
+	cerr << "===============================================" << endl << endl;
 	cerr << "Description: Merges overlapping bed entries into a sinle interval." << endl << endl;
 	cerr << "***NOTE: Only BED3 - BED6 formats allowed.***"<< endl << endl;
 

src/sortBed/sortMain.cpp

@@ -74,14 +74,11 @@ int main(int argc, char* argv[]) {
 
 void ShowHelp(void) {
 	
-	cerr << "=======================================================" << endl;
-	cerr << PROGRAM_NAME << " v" << VERSION << endl ;
-	cerr << "Aaron Quinlan, Ph.D." << endl;
-	cerr << "aaronquinlan@gmail.com" << endl ;
-	cerr << "Hall Laboratory" << endl;
-	cerr << "Biochemistry and Molecular Genetics" << endl;
-	cerr << "University of Virginia" << endl; 
-	cerr << "=======================================================" << endl << endl;
+	cerr << "===============================================" << endl;
+	cerr << " " <<PROGRAM_NAME << " v" << VERSION << endl ;
+	cerr << " Aaron Quinlan, Ph.D. (aaronquinlan@gmail.com)  " << endl ;
+	cerr << " Hall Laboratory, University of Virginia" << endl;
+	cerr << "===============================================" << endl << endl;
 	cerr << "Description: Sorts a BED file by chrom, then by start position." << endl << endl;
 	cerr << "***NOTE: Only BED3 - BED6 formats allowed.***"<< endl << endl;
 

src/windowBed/intersectMain.cpp

+#include "intersectBed.h"
+
+using namespace std;
+
+// define our program name
+#define PROGRAM_NAME "intersectBed"
+
+// define the version
+#define VERSION "1.1.0"
+
+// define our parameter checking macro
+#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)
+
+// function declarations
+void ShowHelp(void);
+
+int main(int argc, char* argv[]) {
+
+	// our configuration variables
+	bool showHelp = false;
+
+	// input files
+	string bedAFile;
+	string bedBFile;
+
+	// input arguments
+	float overlapFraction = 1E-9;
+	int slop = 0;
+
+	bool haveBedA = false;
+	bool haveBedB = false;
+	bool noHit = false;
+	bool anyHit = false;
+	bool writeA = false;	
+	bool writeB = false;
+	bool writeCount = false;
+	bool haveFraction = false;
+	bool haveSlop = false;
+
+	// check to see if we should print out some help
+	if(argc <= 1) showHelp = true;
+
+	for(int i = 1; i < argc; i++) {
+		int parameterLength = (int)strlen(argv[i]);
+
+		if(PARAMETER_CHECK("-h", 2, parameterLength) || 
+		PARAMETER_CHECK("--help", 5, parameterLength)) {
+			showHelp = true;
+		}
+	}
+
+	if(showHelp) ShowHelp();
+
+	// do some parsing (all of these parameters require 2 strings)
+	for(int i = 1; i < argc; i++) {
+
+		int parameterLength = (int)strlen(argv[i]);
+
+		if(PARAMETER_CHECK("-a", 2, parameterLength)) {
+			haveBedA = true;
+			bedAFile = argv[i + 1];
+			i++;
+		}
+		else if(PARAMETER_CHECK("-b", 2, parameterLength)) {
+			haveBedB = true;
+			bedBFile = argv[i + 1];
+			i++;
+		}	
+		else if(PARAMETER_CHECK("-u", 2, parameterLength)) {
+			anyHit = true;
+		}
+		else if(PARAMETER_CHECK("-f", 2, parameterLength)) {
+			haveFraction = true;
+			overlapFraction = atof(argv[i + 1]);
+			i++;
+		}
+		else if(PARAMETER_CHECK("-wa", 3, parameterLength)) {
+			writeA = true;
+		}
+		else if(PARAMETER_CHECK("-wb", 3, parameterLength)) {
+			writeB = true;
+		}
+		else if(PARAMETER_CHECK("-c", 2, parameterLength)) {
+			writeCount = true;
+		}
+		else if (PARAMETER_CHECK("-v", 2, parameterLength)) {
+			noHit = true;
+		}
+		else if (PARAMETER_CHECK("-s", 2, parameterLength)) {
+			haveSlop = true;
+			slop = atoi(argv[i + 1]);
+			i++;
+		}
+		else {
+			cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
+			showHelp = true;
+		}		
+	}
+
+	// make sure we have both input files
+	if (!haveBedA || !haveBedB) {
+		cerr << endl << "*****" << endl << "*****ERROR: Need -a and -b files. " << endl << "*****" << endl;
+		showHelp = true;
+	}
+
+	if (anyHit && noHit) {
+		cerr << endl << "*****" << endl << "*****ERROR: Request either -u OR -v, not both." << endl << "*****" << endl;
+		showHelp = true;
+	}
+
+	if (writeB && writeCount) {
+		cerr << endl << "*****" << endl << "*****ERROR: Request either -wb OR -c, not both." << endl << "*****" << endl;
+		showHelp = true;
+	}
+	
+	if (anyHit && writeCount) {
+		cerr << endl << "*****" << endl << "*****ERROR: Request either -u OR -c, not both." << endl << "*****" << endl;
+		showHelp = true;
+	}
+	
+	if (haveSlop && haveFraction) {
+		cerr << endl << "*****" << endl << "*****ERROR: Request either -s OR -f, not both." << endl << "*****" << endl;
+		showHelp = true;
+	}
+	
+	if (haveSlop && (slop < 0)) {
+		cerr << endl << "*****" << endl << "*****ERROR: Slop (-s) must be positive." << endl << "*****" << endl;
+		showHelp = true;
+	}
+
+	if (!showHelp) {
+
+		BedIntersect *bi = new BedIntersect(bedAFile, bedBFile, anyHit, writeA, writeB, overlapFraction, slop, noHit,  writeCount);
+		bi->IntersectBed();
+		return 0;
+	}
+	else {
+		ShowHelp();
+	}
+}
+
+void ShowHelp(void) {
+
+	cerr << "=======================================================" << endl;
+	cerr << PROGRAM_NAME << " v" << VERSION << endl ;
+	cerr << "Aaron Quinlan, Ph.D." << endl;
+	cerr << "aaronquinlan@gmail.com" << endl ;
+	cerr << "Hall Laboratory" << endl;
+	cerr << "Biochemistry and Molecular Genetics" << endl;
+	cerr << "University of Virginia" << endl; 
+	cerr << "=======================================================" << endl << endl;
+	cerr << "Description: Report overlaps between a.bed and b.bed." << endl << endl;
+	cerr << "***NOTE: Only BED3 - BED6 formats allowed.***"<< endl << endl;
+
+	cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <a.bed> -b <b.bed>" << endl << endl;
+
+	cerr << "OPTIONS: " << endl;
+	cerr << "\t" << "-u\t\t\t"            	<< "Write ORIGINAL a.bed entry ONCE if ANY overlap bed." << endl << "\t\t\t\tIn other words, ignore multiple overlaps." << endl << endl;
+	cerr << "\t" << "-v \t\t\t"             << "Only report those entries in A that have NO OVERLAP in B." << endl << "\t\t\t\tSimilar to grep -v." << endl << endl;
+	cerr << "\t" << "-s (100000)\t\t"	    << "Slop added before and after each entry in A" << endl << "\t\t\t\tUseful for finding overlaps within N bases upstream and downstream." << endl << endl;	
+	cerr << "\t" << "-f (e.g. 0.05)\t\t"	<< "Minimum overlap req'd as fraction of a.bed." << endl << "\t\t\t\tDefault is 1E-9 (effectively 1bp)." << endl << endl;
+	cerr << "\t" << "-c \t\t\t"				<< "For each entry in A, report the number of hits in B while restricting to -f." << endl << "\t\t\t\tReports 0 for A entries that have no overlap with B." << endl << endl;
+	cerr << "\t" << "-wa \t\t\t"			<< "Write the original entry in A for each overlap." << endl << endl;
+	cerr << "\t" << "-wb \t\t\t"			<< "Write the original entry in B for each overlap." << endl << "\t\t\t\tUseful for knowing _what_ A overlaps. Restricted by -f." << endl << endl;
+
+	cerr << "NOTES: " << endl;
+	cerr << "\t" << "-i stdin\t\t"	<< "Allows intersectBed to read BED from stdin.  E.g.: cat a.bed | intersectBed -a stdin -b B.bed" << endl << endl;
+
+
+	// end the program here
+	exit(1);
+
+}