Updated maskFastaFromBed.

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

src/fastaFromBed/fastaFromBedMain.cpp

@@ -109,13 +109,13 @@ void ShowHelp(void) {
 	
 	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 << "USAGE:   " << PROGRAM_NAME << " [OPTIONS] -fi -bed -fo " << 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;
+	cerr << "\t\t-fi\tInput FASTA file" << endl;
+	cerr << "\t\t-bed\tBED file of ranges to extract from -fi" << endl;
+	cerr << "\t\t-fo\tOutput FASTA file" << endl;
+	cerr << "\t\t-name\tUse the BED name field (#4) for the FASTA header" << endl;
 
 
 

src/fastaFromBed/test.fa.out

->myseq
+>chr1:5-10
 AAACC

src/maskFastaFromBed/maskFastaFromBed.cpp

-// 
-//  maskFastaFromBed.cpp
-//  BEDTools
-//  
-//  Created by Aaron Quinlan Spring 2009.
-//  Copyright 2009 Aaron Quinlan. All rights reserved.
-//
-//  Summary:  Mask fasta sequences based on BED intervals.
-//
+/*****************************************************************************
+  maskFastaFromBed.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 "maskFastaFromBed.h"
 

src/maskFastaFromBed/maskFastaFromBed.h

+/*****************************************************************************
+  maskFastaFromBed.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 MASKFASTAFROMBED_H
 #define MASKFASTAFROMBED_H
 

src/maskFastaFromBed/maskFastaFromBedMain.cpp

+/*****************************************************************************
+  maskFastaFromBedMain.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 "maskFastaFromBed.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)) {
 			haveFastaIn = true;
 			fastaInFile = argv[i + 1];
 			i++;
@@ -93,24 +104,21 @@ 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: Mask a fasta file based on BED coordinates." << endl << endl;
 
-	cerr << "Usage: " << PROGRAM_NAME << " -in -out -bed (-soft)" << endl << endl;
+	cerr << endl << "PROGRAM: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl << endl;
+	
+	cerr << "AUTHOR:  Aaron Quinlan (aaronquinlan@gmail.com)" << endl << endl ;
+	
+	cerr << "SUMMARY: Mask a fasta file based on BED coordinates." << endl << endl;
+
+	cerr << "USAGE:   " << PROGRAM_NAME << " [OPTIONS] -fi -out -bed" << endl << endl;
 
 	cerr << "OPTIONS:" << endl;
-	cerr << "\t-in\t\t<FASTA input file>          " << endl;
-	cerr << "\t-bed\t\t<BED coordinates file>          " << endl;
-	cerr << "\t-fo\t\t<FASTA output file>                           " << endl;
-	cerr << "\t-soft\t\tEnforce \"soft\" masking.  That is, instead of masking with Ns," << endl;
+	cerr << "\t\t-fi\tInput FASTA file" << endl;
+	cerr << "\t\t-bed\tBED file of ranges to mask in -fi" << endl;
+	cerr << "\t\t-fo\tOutput FASTA file" << endl;
+	cerr << "\t\t-soft\tEnforce \"soft\" masking.  That is, instead of masking with Ns," << endl;
 	cerr << "\t\t\tmask with lower-case bases." << endl;
-	
-	cerr << "NOTES: " << endl;
-	cerr << "\t***Only tab-delimited BED3 - BED6 formats allowed.***"<< endl << endl;
 
 	// end the program here
 	exit(1);

src/maskFastaFromBed/test.beds

+chr1	5	10	myseq

src/maskFastaFromBed/test.fa

+>chr1
+AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG

src/maskFastaFromBed/test.fa.out

+>chr1
+AAAAANNNNNCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG