Updated mergeBed and bedFile.cpp

	1. Revised usage to 80 chars
	2. GPL headers
	3. Added new stdin logic
	4. Changes logo.
	5. Updated bedFile.cpp's loadBedIntoMapNoBin.  Bug in stdin logic.

src/closestBed/closestMain.cpp

@@ -102,11 +102,10 @@ int main(int argc, char* argv[]) {
 
 void ShowHelp(void) {
 
-	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 << endl << "PROGRAM: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl << endl;
+	
+	cerr << "AUTHOR:  Aaron Quinlan (aaronquinlan@gmail.com)" << endl << endl ;
+
 	cerr << "SUMMARY: For each feature in BED A, finds the closest " << endl;
 	cerr << "\t feature (upstream or downstream) in BED B." << endl << endl;
 

src/intersectBed/intersectMain.cpp

@@ -151,11 +151,10 @@ int main(int argc, char* argv[]) {
 
 void ShowHelp(void) {
 
-	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 << endl << "PROGRAM: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl << endl;
+	
+	cerr << "AUTHOR:  Aaron Quinlan (aaronquinlan@gmail.com)" << endl << endl ;
+
 	cerr << "SUMMARY: Report overlaps between a.bed and b.bed." << endl << endl;
 
 	cerr << "USAGE:   " << PROGRAM_NAME << " [OPTIONS] -a <a.bed> -b <b.bed>" << endl << endl;
@@ -176,7 +175,8 @@ void ShowHelp(void) {
 	cerr 						<< "\t- Similar to \"grep -v.\"" << endl << endl;
 
 	cerr << "  " << "-f\t"		<< "Minimum overlap required as a fraction of A." << endl;
-	cerr 						<< "\t- Default is 1E-9 (i.e., 1bp)." << endl << endl;
+	cerr 						<< "\t- Default is 1E-9 (i.e., 1bp)." << endl;
+	cerr						<< "\t- FLOAT (e.g. 0.50)" << endl << endl;
 
 	cerr << "  " << "-r\t"		<< "Require that the fraction overlap be reciprocal for A and B." << endl;
 	cerr 						<< "\t- In other words, if -f is 0.90 and -r is used, this requires" << endl;

src/mergeBed/a.bed

+chr1	10	20	a
+chr1	15	25	b

src/mergeBed/mergeBed.cpp

-// 
-//  mergeBed.cpp
-//  BEDTools
-//  
-//  Created by Aaron Quinlan Spring 2009.
-//  Copyright 2009 Aaron Quinlan. All rights reserved.
-//
-//  Summary:  Combines overlapping BED entries into a single entry.
-//
+/*****************************************************************************
+  mergeBed.cpp
+
+  (c) 2009 - Aaron Quinlan
+  Hall Laboratory
+  Department of Biochemistry and Molecular Genetics
+  University of Virginia
+  aaronquinlan@gmail.com
+
+  Licenced under the GNU General Public License 2.0+ license.
+******************************************************************************/
 #include "lineFileUtilities.h"
 #include "mergeBed.h"
 
@@ -22,7 +24,6 @@ BedMerge::BedMerge(string &bedFile, bool &numEntries, int &maxDistance, bool &fo
 	this->reportNames = reportNames;
 	
 	this->bed = new BedFile(bedFile);
-
 }
 
 

src/mergeBed/mergeBed.h

+/*****************************************************************************
+  mergeBed.h
+
+  (c) 2009 - Aaron Quinlan
+  Hall Laboratory
+  Department of Biochemistry and Molecular Genetics
+  University of Virginia
+  aaronquinlan@gmail.com
+
+  Licenced under the GNU General Public License 2.0+ license.
+******************************************************************************/
 #include "bedFile.h"
 #include <vector>
 #include <algorithm>

src/mergeBed/mergeMain.cpp

+/*****************************************************************************
+  mergeMain.cpp
+
+  (c) 2009 - Aaron Quinlan
+  Hall Laboratory
+  Department of Biochemistry and Molecular Genetics
+  University of Virginia
+  aaronquinlan@gmail.com
+
+  Licenced under the GNU General Public License 2.0+ license.
+******************************************************************************/
 #include "mergeBed.h"
 #include "version.h"
 
@@ -64,7 +75,7 @@ int main(int argc, char* argv[]) {
 		else if (PARAMETER_CHECK("-s", 2, parameterLength)) {
 			forceStrand = true;
 		}
-		else if (PARAMETER_CHECK("-names", 6, parameterLength)) {
+		else if (PARAMETER_CHECK("-nms", 4, parameterLength)) {
 			reportNames = true;
 		}
 		else {
@@ -97,25 +108,29 @@ int main(int argc, char* argv[]) {
 
 void ShowHelp(void) {
 
-	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 single interval." << endl << endl;
+	cerr << endl << "PROGRAM: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl << endl;
+	
+	cerr << "AUTHOR:  Aaron Quinlan (aaronquinlan@gmail.com)" << endl << endl ;
+	
+	cerr << "SUMMARY: Merges overlapping BED entries into a single interval." << endl << endl;
 
-	cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <input.bed>" << endl << endl;
+	cerr << "USAGE:   " << PROGRAM_NAME << " [OPTIONS] -i <input.bed>" << endl << endl;
 
 	cerr << "OPTIONS: " << endl;
-	cerr << "\t" << "-s\t\t"  << "Force strandedness.  Only report hits in B that overlap A on the same strand." << endl << "\t\t\tBy default, overlaps are reported without respect to strand." << endl << endl;	
-	cerr << "\t" << "-n\t\t"	<< "Report the number of BED entries that were merged. (=1 if no merging occured)" << endl << endl;
-	cerr << "\t" << "-d\t\t"  << "Maximum distance between features allowed for features to be merged. (Default=0)" << endl << endl;
-	cerr << "\t" << "-names\t\t"  << "Report the names of the merged features separated by semicolons." << endl << endl;
-	
+	cerr << "  " << "-s\t"      << "Force strandedness.  That is, only merge features" << endl;
+	cerr						<< "\tthat are the same strand." << endl;
+	cerr						<< "\t- By default, merging is done without respect to strand." << endl << endl;
 
-	cerr << "NOTES: " << endl;
-	cerr << "\t" << "-i stdin\t"	<< "Allows BED file A to be read from stdin.  E.g.: cat a.bed | mergeBed -a stdin -b B.bed" << endl << endl;
-	cerr << "\t***Only tab-delimited BED3 - BED6 formats allowed.***"<< endl << endl;
+	cerr << "  " << "-n\t"		<< "Report the number of BED entries that were merged." << endl;
+	cerr						<< "\t- Note: \"1\" is reported if no merging occured." << endl << endl;
+
+
+	cerr << "  " << "-d\t"  	<< "Maximum distance between features allowed for features to be merged." << endl;
+	cerr 	 					<< "\t- Def. 0. That is, overlapping and/or book-ended features are merged." << endl;
+	cerr						<< "\t- INTEGER" << endl << endl;
+	
+	cerr << "  " << "-nms\t"  	<< "Report the names of the merged features separated by semicolons." << endl << endl;
+	
 
 	// end the program here
 	exit(1);

src/subtractBed/subtractMain.cpp

@@ -107,11 +107,10 @@ int main(int argc, char* argv[]) {
 
 void ShowHelp(void) {
 
-	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 << endl << "PROGRAM: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl << endl;
+	
+	cerr << "AUTHOR:  Aaron Quinlan (aaronquinlan@gmail.com)" << endl << endl ;
+
 	cerr << "SUMMARY: Removes the portion(s) of an interval that is overlapped" << endl;
 	cerr << "\t by another feature(s)." << endl << endl;
 
@@ -119,7 +118,8 @@ void ShowHelp(void) {
 
 	cerr << "OPTIONS: " << endl;
 	cerr << "  " << "-f\t"		<< "Minimum overlap required as a fraction of A." << endl;
-	cerr 						<< "\t- Default is 1E-9 (i.e., 1bp)." << endl << endl;
+	cerr 						<< "\t- Default is 1E-9 (i.e., 1bp)." << endl;
+	cerr						<< "\t- FLOAT (e.g. 0.50)" << endl << endl;
 
 	cerr << "  " << "-s\t"      << "Force strandedness.  That is, only report hits in B that" << endl;
 	cerr						<< "\toverlap A on the same strand." << endl;

src/utils/bedFile/bedFile.cpp

@@ -545,20 +545,19 @@ void BedFile::loadBedFileIntoMapNoBin() {
 	}
 	// Case 2: STDIN.
 	else {
-				
+
 		while (getline(cin, bedLine)) {
 
 			if ((bedLine.find("track") != string::npos) || (bedLine.find("browser") != string::npos)) {
 				continue;
 			}
 			else {
-				vector<string> bedFields;
 				Tokenize(bedLine,bedFields);
-
 				lineNum++;
 
 				if (parseLine(bedEntry, bedFields, lineNum)) {
 					bedEntry.count = 0;
+					bedEntry.minOverlapStart = INT_MAX;
 					this->bedMapNoBin[bedEntry.chrom].push_back(bedEntry);	
 				}
 				bedFields.clear();

src/windowBed/windowMain.cpp

@@ -162,11 +162,10 @@ int main(int argc, char* argv[]) {
 
 void ShowHelp(void) {
 
-	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 << endl << "PROGRAM: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl << endl;
+	
+	cerr << "AUTHOR:  Aaron Quinlan (aaronquinlan@gmail.com)" << endl << endl ;
+
 	cerr << "SUMMARY: Examines a \"window\" around each feature in A and" << endl;
 	cerr << "\t reports all features in B that overlap the window. For each" << endl;
 	cerr << "\t overlap the entire entry in A and B are reported." << endl << endl;
@@ -177,17 +176,20 @@ void ShowHelp(void) {
 	cerr << "  " << "-w\t"		<< "Base pairs added upstream and downstream of each entry" << endl;
 	cerr						<< "\tin A when searching for overlaps in B." << endl;
 	cerr						<< "\t- Creates symterical \"windows\" around A." << endl;		
-	cerr						<< "\t- Default is 1000 bp." << endl << endl;
-	
+	cerr						<< "\t- Default is 1000 bp." << endl;
+	cerr						<< "\t- INTEGER" << endl << endl;
+		
 	cerr << "  " << "-l\t"		<< "Base pairs added upstream (left of) of each entry" << endl;
 	cerr						<< "\tin A when searching for overlaps in B." << endl;	
 	cerr						<< "\t- Allows one to define assymterical \"windows\"." << endl;
-	cerr						<< "\t- Default is 1000 bp." << endl << endl;
+	cerr						<< "\t- Default is 1000 bp." << endl;
+	cerr						<< "\t- INTEGER" << endl << endl;	
 
 	cerr << "  " << "-r\t"		<< "Base pairs added downstream (right of) of each entry" << endl;
 	cerr						<< "\tin A when searching for overlaps in B." << endl;	
 	cerr						<< "\t- Allows one to define assymterical \"windows\"." << endl;
-	cerr						<< "\t- Default is 1000 bp." << endl << endl;
+	cerr						<< "\t- Default is 1000 bp." << endl;
+	cerr						<< "\t- INTEGER" << endl << endl;
 		
 
 	cerr << "  " << "-sw\t"     << "Define -l and -r based on strand.  For example if used, -l 500" << endl;