Updated fastaFromBed.

	1. Revised usage to 80 chars
	2. GPL headers
	3. Added new stdin logic
	4. Changed logo.
	5. Revised the usage statement.

src/fastaFromBed/fastaFromBed.cpp

-// 
-//  fastaFromBed.cpp
-//  BEDTools
-//  
-//  Created by Aaron Quinlan Spring 2009.
-//  Copyright 2009 Aaron Quinlan. All rights reserved.
-//
-//  Summary:  Extract fasta sequences based on BED intervals.
-//
+/*****************************************************************************
+  fastaFromBed.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 "fastaFromBed.h"
 
@@ -21,7 +23,6 @@ Bed2Fa::Bed2Fa(bool &useName, string &dbFile, string &bedFile, string &fastaOutF
 	this->fastaOutFile = fastaOutFile;
 	
 	this->bed = new BedFile(this->bedFile);
-	bed->loadBedFileIntoMapNoBin();
 }
 
 
@@ -50,9 +51,10 @@ void Bed2Fa::ExtractDNA() {
 		exit (1);
 	}	
 	
+	// load the BED file into an unbinned map.
+	bed->loadBedFileIntoMapNoBin();
 
-	/* Read the fastaDb chromosome by chromosome*/
-	
+	//Read the fastaDb chromosome by chromosome
 	string fastaDbLine;
 	string currChrom;
 	string currDNA = "";
@@ -76,9 +78,7 @@ void Bed2Fa::ExtractDNA() {
 				
 					if (!(this->useName)) {
 				    	faOut << ">" << currChrom << ":"
-					  		<< bedList[i].start << "-" << bedList[i].end
-					  		<< "_" << bedList[i].name << endl
-					  		<< dna << endl;
+					  		<< bedList[i].start << "-" << bedList[i].end << endl << dna << endl;
 				  	}
 				  	else {
 				    	faOut << ">" << bedList[i].name << endl << dna << endl;
@@ -101,14 +101,9 @@ void Bed2Fa::ExtractDNA() {
 				
 			string dna = currDNA.substr(bedList[i].start, ((bedList[i].end - bedList[i].start)));
 		
-			//if (bedList[i].strand == "-")  {
-			//	ReverseComplement(dna);
-			//}
 			if (!(this->useName)) {
 		    	faOut << ">" << currChrom << ":"
-			  		<< bedList[i].start << "-" << bedList[i].end
-			  		<< "_" << bedList[i].name << endl
-			  		<< dna << endl;
+			  		<< bedList[i].start << "-" << bedList[i].end << endl << dna << endl;
 		  	}
 		  	else {
 		    	faOut << ">" << bedList[i].name << endl << dna << endl;
@@ -118,3 +113,5 @@ void Bed2Fa::ExtractDNA() {
 	}
 }
 
+
+

src/fastaFromBed/fastaFromBed.h

+/*****************************************************************************
+  fastaFromBed.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.
+******************************************************************************/
 #ifndef FASTAFROMBED_H
 #define FASTAFROMBED_H
 
@@ -23,7 +34,7 @@ public:
 	~Bed2Fa(void);
 
 	void ExtractDNA();
-	
+
 private:
 	
 	bool useName;

src/fastaFromBed/fastaFromBedMain.cpp

+/*****************************************************************************
+  fastaFromBedMain.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 "fastaFromBed.h"
 #include "version.h"
 
@@ -50,7 +61,7 @@ int main(int argc, char* argv[]) {
 
 		int parameterLength = (int)strlen(argv[i]);
 
-		if(PARAMETER_CHECK("-in", 3, parameterLength)) {
+		if(PARAMETER_CHECK("-fi", 3, parameterLength)) {
 			haveFastaDb = true;
 			fastaDbFile = argv[i + 1];
 			i++;
@@ -92,23 +103,21 @@ 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: Extract DNA sequences into a fasta file based on BED coordinates." << endl << endl;
-
-	cerr << "Usage: " << PROGRAM_NAME << " -db -bed -fo -name" << endl << endl;
-
-	cerr << "OPTIONS:" << endl;
-	cerr << "\t-in\t\t<FASTA file for input>" << endl;
-	cerr << "\t-bed\t\t<BED coordinates file>" << endl;
-	cerr << "\t-fo\t\t<FASTA output file>" << endl;
-	cerr << "\t-name\t\tUse the BED name field (#4) for the FASTA header" << endl;
+	cerr << endl << "PROGRAM: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl << endl;
 	
-	cerr << "NOTES: " << endl;
-	cerr << "\t***Only tab-delimited BED3 - BED6 formats allowed.***"<< endl << endl;
+	cerr << "AUTHOR:  Aaron Quinlan (aaronquinlan@gmail.com)" << endl << endl ;
+	
+	cerr << "SUMMARY: Extract DNA sequences into a fasta file based on BED coordinates." << endl << endl;
+
+	cerr << "USAGE:   " << PROGRAM_NAME << " -fi (req'd) -bed (req'd) -fo (req'd) -name (opt.)" << endl << endl;
+
+	cerr << "OPTIONS: " << endl;
+	cerr << "\t-fi\t\tInput FASTA file" << endl;
+	cerr << "\t-bed\t\tBED file of ranges to extract from -fi" << endl;
+	cerr << "\t-fo\t\tOutput FASTA file" << endl;
+	cerr << "\t-name\t\tUse the BED name field (#4) for the FASTA header" << endl;
+
+
 
 	// end the program here
 	exit(1);

src/fastaFromBed/test.beds

+chr1	5	10	myseq

src/fastaFromBed/test.fa

+>chr1
+AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG

src/fastaFromBed/test.fa.out

+>myseq
+AAACC