Command line option formatting standardized.

src/coverageBed/coverageMain.cpp

@@ -99,7 +99,7 @@ void ShowHelp(void) {
 	cerr << "Author:  Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
 	
 	cerr << "Summary: Returns the depth and breadth of coverage of features from A" << endl;
-	cerr << "\t\t on the intervals in B." << endl << endl;
+	cerr << "\t on the intervals in B." << endl << endl;
 	
 	cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -a <a.bed> -b <b.bed>" << endl << endl;
 

src/fastaFromBed/fastaFromBedMain.cpp

@@ -112,9 +112,9 @@ void ShowHelp(void) {
 	cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -fi -bed -fo " << endl << endl;
 
 	cerr << "Options: " << endl;
-	cerr << "\t-fi\t\tInput FASTA file" << endl;
+	cerr << "\t-fi\tInput FASTA file" << endl;
 	cerr << "\t-bed\tBED file of ranges to extract from -fi" << endl;
-	cerr << "\t-fo\t\tOutput FASTA file" << endl;
+	cerr << "\t-fo\tOutput FASTA file" << endl;
 	cerr << "\t-name\tUse the BED name field (#4) for the FASTA header" << endl;
 
 

src/genomeCoverageBed/genomeCoverageMain.cpp

@@ -114,12 +114,12 @@ void ShowHelp(void) {
 	cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -i <bed> -g <genome>" << endl << endl;
 	
 	cerr << "Options: " << endl;
-	cerr << "\t-d\t\t"	     	<< "Report the depth at each genome position." << endl;
-	cerr 						<< "\t\t\tDefault behavior is to report a histogram." << endl << endl;
+	cerr << "\t-d\t"	     	<< "Report the depth at each genome position." << endl;
+	cerr 						<< "\t\tDefault behavior is to report a histogram." << endl << endl;
 
 	cerr << "\t-max\t"          << "Combine all positions with a depth >= max into" << endl;
-	cerr						<< "\t\t\ta single bin in the histogram." << endl;
-	cerr						<< "\t\t\t- (INTEGER)" << endl << endl;
+	cerr						<< "\t\ta single bin in the histogram." << endl;
+	cerr						<< "\t\t- (INTEGER)" << endl << endl;
 
 	cerr << "Notes: " << endl;
 	cerr << "\t(1)  The genome file should tab delimited and structured as follows:" << endl;

src/intersectBed/a.bed

+# stuff
 chr1	0	12000	a	1	+

src/intersectBed/b.bed

-chr1	50	150	b	2	-	same	to 	you
+chr1	50	150	b	2	-

src/linksBed/linksMain.cpp

@@ -107,13 +107,13 @@ void ShowHelp(void) {
 	cerr << "Options: " << endl;
 	cerr << "\t-base\t"	<< "The browser basename.  Default: http://genome.ucsc.edu " << endl;
 	cerr << "\t-org\t"	<< "The organism. Default: human" << endl;
-	cerr << "\t-db\t\t"	<< "The build.  Default: hg18" << endl << endl;
+	cerr << "\t-db\t"	<< "The build.  Default: hg18" << endl << endl;
 	
 	cerr << "Example: " << endl;
-	cerr << "\t" << "By default, the links created will point to the human (hg18) UCSC browser." << endl;
+	cerr << "\t" << "By default, the links created will point to human (hg18) UCSC browser." << endl;
 	cerr << 		"\tIf you have a local mirror, you can override this behavior by supplying" << endl;
 	cerr <<			"\tthe -base, -org, and -db options."  << endl << endl;
-	cerr << "\t" << "For example, if the main URL of your local mirror for mouse MM9 is called: " << endl;
+	cerr << "\t" << "For example, if the URL of your local mirror for mouse MM9 is called: " << endl;
 	cerr << 		"\thttp://mymirror.myuniversity.edu, then you would use the following:" << endl;
 	cerr << 		"\t" << "-base http://mymirror.myuniversity.edu" << endl;
 	cerr << 		"\t" << "-org mouse" << endl; 

src/maskFastaFromBed/maskFastaFromBedMain.cpp

@@ -114,11 +114,11 @@ void ShowHelp(void) {
 	cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -fi -out -bed" << endl << endl;
 
 	cerr << "Options:" << endl;
-	cerr << "\t-fi\t\tInput FASTA file" << endl;
+	cerr << "\t-fi\tInput FASTA file" << endl;
 	cerr << "\t-bed\tBED file of ranges to mask in -fi" << endl;
-	cerr << "\t-fo\t\tOutput FASTA file" << endl;
+	cerr << "\t-fo\tOutput FASTA file" << endl;
 	cerr << "\t-soft\tEnforce \"soft\" masking.  That is, instead of masking with Ns," << endl;
-	cerr << "\t\t\tmask with lower-case bases." << endl;
+	cerr << "\t\tmask with lower-case bases." << endl;
 
 	// end the program here
 	exit(1);

src/pairToBed/pairToBedMain.cpp

@@ -176,11 +176,11 @@ void ShowHelp(void) {
 	cerr								<< "\t\tispan\tReport overlaps between [end1, start2] of A and B." << endl; 
 	cerr									<< "\t\t\t- Note: If chrom1 <> chrom2, entry is ignored." << endl;
 	cerr								<< "\t\tospan\tReport overlaps between [start1, end2] of A and B." << endl; 
-	cerr									<< "\t\t\t- Note: If chrom1 <> chrom2, entry is ignored." << endl << endl;
-	cerr								<< "\t\tnotispan\tReport A if ispan of A doesn't overlap B." << endl; 
 	cerr									<< "\t\t\t- Note: If chrom1 <> chrom2, entry is ignored." << endl;
+	cerr								<< "\t\tnotispan\tReport A if ispan of A doesn't overlap B." << endl; 
+	cerr									<< "\t\t\t\t- Note: If chrom1 <> chrom2, entry is ignored." << endl;
 	cerr								<< "\t\tnotospan\tReport A if ospan of A doesn't overlap B." << endl; 
-	cerr									<< "\t\t\t- Note: If chrom1 <> chrom2, entry is ignored." << endl << endl;
+	cerr									<< "\t\t\t\t- Note: If chrom1 <> chrom2, entry is ignored." << endl << endl;
 		
 	cerr << "Refer to the BEDTools manual for BEDPE format." << endl << endl;
 

src/pairToPair/pairToPairMain.cpp

@@ -135,11 +135,11 @@ void ShowHelp(void) {
 	cerr << "\t-f\t"	    			<< "Minimum overlap required as fraction of A (e.g. 0.05)." << endl;
 	cerr 								<< "\t\tDefault is 1E-9 (effectively 1bp)." << endl << endl;
 
-	cerr << "\t-type \t"				<< "Approach to reporting overlaps between A and B." << endl;
-	cerr 								<< "\t\tneither\t\tReport overlaps if neither end of A overlaps B." << endl << endl;
+	cerr << "\t-type \t"				<< "Approach to reporting overlaps between A and B." << endl << endl;
+	cerr 								<< "\t\tneither\tReport overlaps if neither end of A overlaps B." << endl;
 
-	cerr 								<< "\t\tboth\t\tReport overlaps if both ends of A overlap B." << endl;
-	cerr									<< "\t\t\t\t- Default." << endl;
+	cerr 								<< "\t\tboth\tReport overlaps if both ends of A overlap B." << endl;
+	cerr									<< "\t\t\t- Default." << endl << endl;
 
 	cerr << "\t-is\t"	    			<< "Ignore strands when searching for overlaps." << endl;
 	cerr 								<< "\t\t- By default, strands are enforced." << endl << endl;

src/shuffleBed/shuffleBedMain.cpp

@@ -119,14 +119,14 @@ void ShowHelp(void) {
 	
 	cerr << "Options: " << endl;
 	cerr << "\t-excl\t"           	<< "A BED file of coordinates in which features in -i" << endl;
-	cerr							<< "\t\t\tshould not be placed (e.g. gaps.bed)." << endl << endl;
+	cerr							<< "\t\tshould not be placed (e.g. gaps.bed)." << endl << endl;
 
 	cerr << "\t-chrom\t"      		<< "Keep features in -i on the same chromosome."<< endl; 
-	cerr							<< "\t\t\t- By default, the chrom and position are randomly chosen." << endl << endl;
+	cerr							<< "\t\t- By default, the chrom and position are randomly chosen." << endl << endl;
 
 	cerr << "\t-seed\t"     		<< "Supply an integer seed for the shuffling." << endl; 
-	cerr							<< "\t\t\t- By default, the seed is chosen automatically." << endl;
-	cerr							<< "\t\t\t- (INTEGER)" << endl << endl;
+	cerr							<< "\t\t- By default, the seed is chosen automatically." << endl;
+	cerr							<< "\t\t- (INTEGER)" << endl << endl;
 
 
 	cerr << "Notes: " << endl;

src/slopBed/slopBedMain.cpp

@@ -138,7 +138,7 @@ void ShowHelp(void) {
 	cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -i <bed> -g <genome> [-b <int> or (-l and -r)]" << endl << endl;
 	
 	cerr << "Options: " << endl;
-	cerr << "\t-b\t"            	<< "Increase the BED entry by the same number base pairs in each direction." << endl;
+	cerr << "\t-b\t"            	<< "Increase the BED entry by -b base pairs in each direction." << endl;
 	cerr 							<< "\t\t- (Integer)" << endl;
 		
 	cerr << "\t-l\t"            	<< "The number of base pairs to subtract from the start coordinate." << endl;
@@ -152,12 +152,12 @@ void ShowHelp(void) {
 	cerr							<< "\t\tit will add 500 bp downstream.  Default = false." << endl << endl;	
 
 	cerr << "Notes: " << endl;
-	cerr << "\t(1)  Starts will be set to 0 if the requested slop would force it below 0." << endl;
-	cerr << "\t(2)  Ends will be set to the chromosome length if the requested slop would" << endl;
-	cerr <<	       "\t\t force it above the max chrom length." << endl;
+	cerr << "\t(1)  Starts will be set to 0 if options would force it below 0." << endl;
+	cerr << "\t(2)  Ends will be set to the chromosome length if  requested slop would" << endl;
+	cerr <<	       "\tforce it above the max chrom length." << endl;
 
 	cerr << "\t(3)  The genome file should tab delimited and structured as follows:" << endl;
-	cerr << "\t     <chromName><TAB><chromSize>" << endl << endl;
+	cerr << "\n\t<chromName><TAB><chromSize>" << endl << endl;
 	cerr << "\tFor example, Human (hg19):" << endl;
 	cerr << "\tchr1\t249250621" << endl;
 	cerr << "\tchr2\t243199373" << endl;