Added new logic to handle stdin or file in slopBed.

   This becomes the new model for handling files/stdin,
   rather than duplicating the main logic of each porgram
   in a block for files and a block for stdin.

   Much slicker.

RELEASE_HISTORY

+Version 2.3.2 (11/25/2009)
+Fixed a bug in subtractBed that prevent a file from subtracting itself when the following is used:
+	$ subtractBed -a test.bed -b test.bed
+
 Version 2.3.1 (11/19/2009)
 Fixed a typo in closestBed that caused all nearby features to be returned instead of just the closest one.
 

genomes/human.hg18.genome

+chr1	247249719
+chr1_random	1663265
+chr10	135374737
+chr10_random	113275
+chr11	134452384
+chr11_random	215294
+chr12	132349534
+chr13	114142980
+chr13_random	186858
+chr14	106368585
+chr15	100338915
+chr15_random	784346
+chr16	88827254
+chr16_random	105485
+chr17	78774742
+chr17_random	2617613
+chr18	76117153
+chr18_random	4262
+chr19	63811651
+chr19_random	301858
+chr2	242951149
+chr2_random	185571
+chr20	62435964
+chr21	46944323
+chr21_random	1679693
+chr22	49691432
+chr22_random	257318
+chr22_h2_hap1	63661
+chr3	199501827
+chr3_random	749256
+chr4	191273063
+chr4_random	842648
+chr5	180857866
+chr5_random	143687
+chr5_h2_hap1	1794870
+chr6	170899992
+chr6_random	1875562
+chr6_cox_hap1	4731698
+chr6_qbl_hap2	4565931
+chr7	158821424
+chr7_random	549659
+chr8	146274826
+chr8_random	943810
+chr9	140273252
+chr9_random	1146434
+chrM	16571
+chrX	154913754
+chrX_random	1719168
+chrY	57772954
+

genomes/human.hg19.genome

+chr1	249250621
+chr2	243199373
+chr3	198022430
+chr4	191154276
+chr5	180915260
+chr6	171115067
+chr7	159138663
+chrX	155270560
+chr8	146364022
+chr9	141213431
+chr10	135534747
+chr11	135006516
+chr12	133851895
+chr13	115169878
+chr14	107349540
+chr15	102531392
+chr16	90354753
+chr17	81195210
+chr18	78077248
+chr20	63025520
+chrY	59373566
+chr19	59128983
+chr22	51304566
+chr21	48129895
+chr6_ssto_hap7	4928567
+chr6_mcf_hap5	4833398
+chr6_cox_hap2	4795371
+chr6_mann_hap4	4683263
+chr6_apd_hap1	4622290
+chr6_qbl_hap6	4611984
+chr6_dbb_hap3	4610396
+chr17_ctg5_hap1	1680828
+chr4_ctg9_hap1	590426
+chr1_gl000192_random	547496
+chrUn_gl000225	211173
+chr4_gl000194_random	191469
+chr4_gl000193_random	189789
+chr9_gl000200_random	187035
+chrUn_gl000222	186861
+chrUn_gl000212	186858
+chr7_gl000195_random	182896
+chrUn_gl000223	180455
+chrUn_gl000224	179693
+chrUn_gl000219	179198
+chr17_gl000205_random	174588
+chrUn_gl000215	172545
+chrUn_gl000216	172294
+chrUn_gl000217	172149
+chr9_gl000199_random	169874
+chrUn_gl000211	166566
+chrUn_gl000213	164239
+chrUn_gl000220	161802
+chrUn_gl000218	161147
+chr19_gl000209_random	159169
+chrUn_gl000221	155397
+chrUn_gl000214	137718
+chrUn_gl000228	129120
+chrUn_gl000227	128374
+chr1_gl000191_random	106433
+chr19_gl000208_random	92689
+chr9_gl000198_random	90085
+chr17_gl000204_random	81310
+chrUn_gl000233	45941
+chrUn_gl000237	45867
+chrUn_gl000230	43691
+chrUn_gl000242	43523
+chrUn_gl000243	43341
+chrUn_gl000241	42152
+chrUn_gl000236	41934
+chrUn_gl000240	41933
+chr17_gl000206_random	41001
+chrUn_gl000232	40652
+chrUn_gl000234	40531
+chr11_gl000202_random	40103
+chrUn_gl000238	39939
+chrUn_gl000244	39929
+chrUn_gl000248	39786
+chr8_gl000196_random	38914
+chrUn_gl000249	38502
+chrUn_gl000246	38154
+chr17_gl000203_random	37498
+chr8_gl000197_random	37175
+chrUn_gl000245	36651
+chrUn_gl000247	36422
+chr9_gl000201_random	36148
+chrUn_gl000235	34474
+chrUn_gl000239	33824
+chr21_gl000210_random	27682
+chrUn_gl000231	27386
+chrUn_gl000229	19913
+chrM	16571
+chrUn_gl000226	15008
+chr18_gl000207_random	4262
+

src/linksBed/linksMain.cpp

@@ -104,7 +104,7 @@ void ShowHelp(void) {
 	cerr << "\t" << "-db\t\t"	<< "The build.  Default: hg18" << endl << endl;
 
 	cerr << "NOTES: " << endl;
-	cerr << "\t" << "-i stdin\t"	<< "Allows BED file A to be read from stdin.  E.g.: cat a.bed | linksBed -i stdin > out.html" << endl << endl;
+	cerr << "\t" << "-i stdin\t"	<< "Allows BED file to be read from stdin.  E.g.: cat a.bed | linksBed -i stdin > out.html" << endl << endl;
 	cerr << "\t***Only tab-delimited BED3 - BED6 formats allowed.***"<< endl << endl;
 	
 	cerr << "EXAMPLE: " << endl;

src/slopBed/slopBed.cpp

@@ -34,7 +34,7 @@ BedSlop::~BedSlop(void) {
 
 
 
-void BedSlop::ProcessBed() {
+void BedSlop::DetermineBedInput() {
 
 
 	/* open the GENOME file for reading.
@@ -57,17 +57,27 @@ void BedSlop::ProcessBed() {
 		}
 	}
 
-	ifstream beds(this->bedFile.c_str(), ios::in);
-	if ( !beds ) {
-		cerr << "Error: The requested bed file (" <<this->bedFile << ") could not be opened. Exiting!" << endl;
-		exit (1);
+	if (this->bedFile != "stdin") {   // process a file
+		ifstream beds(this->bedFile.c_str(), ios::in);
+		if ( !beds ) {
+			cerr << "Error: The requested bed file (" << this->bedFile << ") could not be opened. Exiting!" << endl;
+			exit (1);
+		}
+		ProcessBed(beds);
+	}
+	else {   // process stdin
+		ProcessBed(cin);		
 	}
+}
+
+
+void BedSlop::ProcessBed(istream &bedInput) {
 	
 	BED bedEntry;     // used to store the current BED line from the BED file.
 	int lineNum = 0;
 	string bedLine;	  // used to store the current (unparsed) line from the BED file.
 		
-	while (getline(beds, bedLine)) {
+	while (getline(bedInput, bedLine)) {
 		
 		vector<string> bedFields;
 		Tokenize(bedLine,bedFields);

src/slopBed/slopBed.h

@@ -22,8 +22,10 @@ public:
 	// destructor
 	~BedSlop(void);
 
-	void ProcessBed();
-	
+	void DetermineBedInput();
+
+	void ProcessBed(istream &bedInput);
+		
 	// method to add requested "slop" to each BED entry
 	void AddSlop(BED &);
 	

src/slopBed/slopBedMain.cpp

@@ -106,7 +106,7 @@ int main(int argc, char* argv[]) {
 	}	
 	if (!showHelp) {
 		BedSlop *bc = new BedSlop(bedFile, genomeFile, forceStrand, leftSlop, rightSlop);
-		bc->ProcessBed();		
+		bc->DetermineBedInput();		
 		
 		return 0;
 	}
@@ -134,13 +134,14 @@ void ShowHelp(void) {
 
 	cerr << "NOTES: " << endl;
 	cerr << "\t1.  Starts will be corrected to 0 if the requested slop would force it below 0." << endl;
-	cerr << "\t2.  Ends will be corrected to the chromosome length if the requested slop would force it above the max chrom length." << endl << endl;
+	cerr << "\t2.  Ends will be corrected to the chromosome length if the requested slop would force it above the max chrom length." << endl;
 	cerr << "\t3.  The genome file should tab delimited and structured as follows: <chr><TAB><size>. For example, Mus musculus:" << endl;
 	cerr << "\t\tchr1\t197195432" << endl;
 	cerr << "\t\tchr2\t181748087" << endl;
 	cerr << "\t\t..." << endl;
-	cerr << "\t\tchrY_random\t58682461" << endl << endl;
-	cerr << "\t4.  ***Only tab-delimited BED3 - BED6 formats allowed.***"<< endl << endl;
+	cerr << "\t\tchrY_random\t58682461" << endl;
+	cerr << "\t4.  -i stdin\t"	<< "Allows BED file to be read from stdin.  E.g.: cat a.bed | slopBed -i stdin" << endl;
+	cerr << "\t5.  ***Only tab-delimited BED3 - BED6 formats allowed.***"<< endl << endl;
 
 	cerr << "TIPS:" << endl;
 	cerr << "\tOne can use the UCSC Genome Browser's MySQL database to extract chromosome sizes. For example, H. sapiens:" << endl << endl;

src/subtractBed/a.bed

+chr1	100	200
+

src/subtractBed/b.bed

+chr1	150	250
+