diff --git a/bin/coverageBed b/bin/coverageBed
index 1583bfbbc1fe4b4f2d4c16fbb9ba2d0e733911e2..701c8656e2b34da767e70f46ccfe404a4db6aa73 100755
Binary files a/bin/coverageBed and b/bin/coverageBed differ
diff --git a/obj/bedFile.o b/obj/bedFile.o
index 1e7a0d65d39c05d154bd0bce50726c041381f3cf..3dbf5bff0cc703d0646bfd6150484505d9ea6105 100644
Binary files a/obj/bedFile.o and b/obj/bedFile.o differ
diff --git a/obj/coverageBed.o b/obj/coverageBed.o
index 4aa3ae956dd4470d8116096b7a45745f1092149b..d06f390598f3a5fd967228e9d62dcf704b6c9c67 100644
Binary files a/obj/coverageBed.o and b/obj/coverageBed.o differ
diff --git a/obj/coverageMain.o b/obj/coverageMain.o
index e7654258126e6813611504b7efff92cccc15d1a3..29e96bfc48e9007087da1e639648d699533dce05 100644
Binary files a/obj/coverageMain.o and b/obj/coverageMain.o differ
diff --git a/src/coverageBed/a.bed b/src/coverageBed/a.bed
new file mode 100644
index 0000000000000000000000000000000000000000..f7890ff1342ff62bebee6488db8cc09f0589de01
--- /dev/null
+++ b/src/coverageBed/a.bed
@@ -0,0 +1,4 @@
+chr1 10 20
+chr1 20 30
+chr1 30 40
+
diff --git a/src/coverageBed/b.bed b/src/coverageBed/b.bed
new file mode 100644
index 0000000000000000000000000000000000000000..4d05dacdf0fb9aa6a2e9c72e02cef71c4223771f
--- /dev/null
+++ b/src/coverageBed/b.bed
@@ -0,0 +1,2 @@
+chr1 0 100
+chr2 0 100
diff --git a/src/coverageBed/coverageBed.cpp b/src/coverageBed/coverageBed.cpp
index 4eb85c5f2b72d020a7391a2127f8a525dcccdda6..48ebf088456b98007d30b0b25a0e15e2035003a8 100755
--- a/src/coverageBed/coverageBed.cpp
+++ b/src/coverageBed/coverageBed.cpp
@@ -1,16 +1,19 @@
-//
-// coverageBed.cpp
-// BEDTools
-//
-// Created by Aaron Quinlan Spring 2009.
-// Copyright 2009 Aaron Quinlan. All rights reserved.
-//
-//
+/*****************************************************************************
+ coverageBed.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 "coverageBed.h"
-BedGraph::BedGraph(string &bedAFile, string &bedBFile, bool &forceStrand) {
+BedCoverage::BedCoverage(string &bedAFile, string &bedBFile, bool &forceStrand) {
this->bedAFile = bedAFile;
this->bedBFile = bedBFile;
@@ -23,75 +26,43 @@ BedGraph::BedGraph(string &bedAFile, string &bedBFile, bool &forceStrand) {
-BedGraph::~BedGraph(void) {
+BedCoverage::~BedCoverage(void) {
}
-void BedGraph::GraphBed() {
-
+void BedCoverage::GetCoverage(istream &bedInput) {
+
// load the "B" bed file into a map so
// that we can easily compare "A" to it for overlaps
bedB->loadBedFileIntoMap();
-
- string bedLine;
- BED bedEntry;
- int lineNum = 0;
-
- // are we dealing with a file?
- if (bedA->bedFile != "stdin") {
-
- ifstream bed(bedA->bedFile.c_str(), ios::in);
- if ( !bed ) {
- cerr << "Error: The requested bed file (" <<bedA->bedFile << ") could not be opened. Exiting!" << endl;
- exit (1);
- }
+ string bedLine;
+ int lineNum = 0; // current input line number
+ vector<string> bedFields; // vector for a BED entry
- BED a;
- while (getline(bed, bedLine)) {
+ bedFields.reserve(12);
- if ((bedLine.find("track") != string::npos) || (bedLine.find("browser") != string::npos)) {
- continue;
- }
- else {
- vector<string> bedFields;
- Tokenize(bedLine,bedFields);
- lineNum++;
- // process the feature in A IFF it's valid.
- if (bedA->parseBedLine(a, bedFields, lineNum)) {
-
- // increment the count of overlaps for each feature in B that
- // overlaps the current A interval
- bedB->countHits(bedB->bedMap[a.chrom], a, this->forceStrand);
- }
- }
- }
- }
- // A is being passed via stdin.
- else {
+ BED a;
+ // process each entry in A
+ while (getline(bedInput, bedLine)) {
+
+ lineNum++;
+ Tokenize(bedLine,bedFields);
- BED a;
- while (getline(cin, bedLine)) {
-
- if ((bedLine.find("track") != string::npos) || (bedLine.find("browser") != string::npos)) {
- continue;
- }
- else {
- vector<string> bedFields;
- Tokenize(bedLine,bedFields);
- lineNum++;
- // process the feature in A IFF it's valid.
- if (bedA->parseBedLine(a, bedFields, lineNum)) {
-
- // increment the count of overlaps for each feature in B that
- // overlaps the current A interval
- bedB->countHits(bedB->bedMap[a.chrom], a, this->forceStrand);
- }
- }
- }
+ // find the overlaps with B if it's a valid BED entry.
+ if (bedA->parseLine(a, bedFields, lineNum)) {
+
+ // increment the count of overlaps for each feature in B that
+ // overlaps the current A interval
+ bedB->countHits(bedB->bedMap[a.chrom], a, this->forceStrand);
+ }
+ // reset for the next input line
+ bedFields.clear();
}
+
+
// now, report the count of hist for each feature in B.
for (masterBedMap::iterator c = bedB->bedMap.begin(); c != bedB->bedMap.end(); ++c) {
map<int, vector<BED> > bin2Beds = c->second;
@@ -135,3 +106,18 @@ void BedGraph::GraphBed() {
}
+void BedCoverage::DetermineBedInput() {
+ if (bedA->bedFile != "stdin") { // process a file
+ ifstream beds(bedA->bedFile.c_str(), ios::in);
+ if ( !beds ) {
+ cerr << "Error: The requested bed file (" << bedA->bedFile << ") could not be opened. Exiting!" << endl;
+ exit (1);
+ }
+ GetCoverage(beds);
+ }
+ else { // process stdin
+ GetCoverage(cin);
+ }
+}
+
+
diff --git a/src/coverageBed/coverageBed.h b/src/coverageBed/coverageBed.h
index 785fb6faf22e93f8b7c465bfab93ba754ad105a2..e4654e646e2b0936b8f8922f356243b58e77c8e5 100755
--- a/src/coverageBed/coverageBed.h
+++ b/src/coverageBed/coverageBed.h
@@ -1,3 +1,14 @@
+/*****************************************************************************
+ coverageBed.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 COVERAGEBED_H
#define COVERAGEBED_H
@@ -12,18 +23,19 @@ using namespace std;
//************************************************
// Class methods and elements
//************************************************
-class BedGraph {
+class BedCoverage {
public:
// constructor
- BedGraph(string &, string &, bool &);
+ BedCoverage(string &, string &, bool &);
// destructor
- ~BedGraph(void);
+ ~BedCoverage(void);
- void GraphBed();
+ void GetCoverage(istream &bedInput);
+ void DetermineBedInput();
private:
diff --git a/src/coverageBed/coverageMain.cpp b/src/coverageBed/coverageMain.cpp
index 4dfef4c96871e25f326faab481acf29ae5f6f636..81ced62074a392e7431094fb8831463945981fe9 100755
--- a/src/coverageBed/coverageMain.cpp
+++ b/src/coverageBed/coverageMain.cpp
@@ -1,3 +1,14 @@
+/*****************************************************************************
+ coverageMain.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 "coverageBed.h"
#include "version.h"
@@ -72,8 +83,8 @@ int main(int argc, char* argv[]) {
if (!showHelp) {
- BedGraph *bg = new BedGraph(bedAFile, bedBFile, forceStrand);
- bg->GraphBed();
+ BedCoverage *bg = new BedCoverage(bedAFile, bedBFile, forceStrand);
+ bg->DetermineBedInput();
return 0;
}
else {
@@ -85,22 +96,17 @@ void ShowHelp(void) {
//cout << "\t" << beds[i].count << "\t" << (length-zeroDepthCount) << "\t" << length << "\t" << (float) (length-zeroDepthCount)/length << endl;
- 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: Returns the depth and breadth of coverage of features from A" << endl;
- cerr << "on the intervals in B." << endl << endl;
+ cerr << endl << "PROGRAM: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl << endl;
- cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <a.bed> -b <b.bed>" << endl << endl;
-
- cerr << "NOTES: " << endl;
- cerr << "\t" << "-i stdin\t\t" << "Allows BED file A to be read from stdin. E.g.: cat a.bed | coverageBed -a stdin -b B.bed" << endl << endl;
- cerr << "\t***Only tab-delimited BED3 - BED6 formats allowed.***"<< endl << endl;
+ cerr << "AUTHOR: Aaron Quinlan (aaronquinlan@gmail.com)" << endl << endl ;
+
+ cerr << "SUMMARY: Returns the depth and breadth of coverage of features from A" << endl;
+ cerr << "\t on the intervals in B." << endl << endl;
+
+ cerr << "USAGE: " << PROGRAM_NAME << " [OPTIONS] -a <a.bed> -b <b.bed>" << endl << endl;
- cerr << "OUTPUT: " << endl;
- cerr << "\t" << "After each entry in B, reports: " << endl;
+ cerr << "OUTPUT: " << endl;
+ cerr << "\t" << " After each entry in B, reports: " << endl;
cerr << "\t 1) The number of overlapping entries in A." << endl;
cerr << "\t 2) The number of bases in B that had non-zero coverage." << endl;
cerr << "\t 3) The length of the entry in B." << endl;
diff --git a/src/mergeBed/a.bed b/src/mergeBed/a.bed
index c2a8b2733b0e0196c294ac5f594b0725db4ba9b8..580802f1203c760cb418e6e4e06b52aa903741ab 100644
--- a/src/mergeBed/a.bed
+++ b/src/mergeBed/a.bed
@@ -1,2 +1,3 @@
-chr1 10 20 a
-chr1 15 25 b
+chr1 100 200 A1
+chr1 150 300 A2
+chr1 250 500 A3
diff --git a/src/mergeBed/b.bed b/src/mergeBed/b.bed
new file mode 100644
index 0000000000000000000000000000000000000000..65d98810f03122c4f2fed316342d9af4632e6e1b
--- /dev/null
+++ b/src/mergeBed/b.bed
@@ -0,0 +1,3 @@
+chr1 100 200
+chr1 501 1000
+
diff --git a/src/mergeBed/genes.gff b/src/mergeBed/genes.gff
new file mode 100644
index 0000000000000000000000000000000000000000..4d8883e5f69022f5d9753ef47cc1aee9e24fb2bb
--- /dev/null
+++ b/src/mergeBed/genes.gff
@@ -0,0 +1,1462 @@
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+chr1 hg19_knownGene CDS 1233947 1233999 0.000000 - 0 gene_id "uc001ady.2"; transcript_id "uc001ady.2";
+chr1 hg19_knownGene start_codon 1233997 1233999 0.000000 - . gene_id "uc001ady.2"; transcript_id "uc001ady.2";
+chr1 hg19_knownGene exon 1233947 1234335 0.000000 - . gene_id "uc001ady.2"; transcript_id "uc001ady.2";
+chr1 hg19_knownGene CDS 1228944 1229088 0.000000 - 1 gene_id "uc001aea.2"; transcript_id "uc001aea.2";
+chr1 hg19_knownGene exon 1227764 1229088 0.000000 - . gene_id "uc001aea.2"; transcript_id "uc001aea.2";
+chr1 hg19_knownGene CDS 1229203 1229313 0.000000 - 1 gene_id "uc001aea.2"; transcript_id "uc001aea.2";
+chr1 hg19_knownGene exon 1229203 1229313 0.000000 - . gene_id "uc001aea.2"; transcript_id "uc001aea.2";
+chr1 hg19_knownGene CDS 1229470 1229579 0.000000 - 0 gene_id "uc001aea.2"; transcript_id "uc001aea.2";
+chr1 hg19_knownGene exon 1229470 1229579 0.000000 - . gene_id "uc001aea.2"; transcript_id "uc001aea.2";
+chr1 hg19_knownGene CDS 1229782 1230008 0.000000 - 2 gene_id "uc001aea.2"; transcript_id "uc001aea.2";
+chr1 hg19_knownGene exon 1229782 1230008 0.000000 - . gene_id "uc001aea.2"; transcript_id "uc001aea.2";
+chr1 hg19_knownGene CDS 1230827 1230934 0.000000 - 2 gene_id "uc001aea.2"; transcript_id "uc001aea.2";
+chr1 hg19_knownGene exon 1230827 1230934 0.000000 - . gene_id "uc001aea.2"; transcript_id "uc001aea.2";
+chr1 hg19_knownGene CDS 1231116 1231318 0.000000 - 1 gene_id "uc001aea.2"; transcript_id "uc001aea.2";
+chr1 hg19_knownGene exon 1231116 1231318 0.000000 - . gene_id "uc001aea.2"; transcript_id "uc001aea.2";
+chr1 hg19_knownGene CDS 1231395 1231489 0.000000 - 0 gene_id "uc001aea.2"; transcript_id "uc001aea.2";
+chr1 hg19_knownGene exon 1231395 1231489 0.000000 - . gene_id "uc001aea.2"; transcript_id "uc001aea.2";
+chr1 hg19_knownGene CDS 1231591 1231660 0.000000 - 1 gene_id "uc001aea.2"; transcript_id "uc001aea.2";
+chr1 hg19_knownGene exon 1231591 1231660 0.000000 - . gene_id "uc001aea.2"; transcript_id "uc001aea.2";
+chr1 hg19_knownGene CDS 1231805 1232013 0.000000 - 0 gene_id "uc001aea.2"; transcript_id "uc001aea.2";
+chr1 hg19_knownGene exon 1231805 1232013 0.000000 - . gene_id "uc001aea.2"; transcript_id "uc001aea.2";
+chr1 hg19_knownGene CDS 1233202 1233313 0.000000 - 1 gene_id "uc001aea.2"; transcript_id "uc001aea.2";
+chr1 hg19_knownGene exon 1233202 1233313 0.000000 - . gene_id "uc001aea.2"; transcript_id "uc001aea.2";
+chr1 hg19_knownGene CDS 1233393 1233493 0.000000 - 0 gene_id "uc001aea.2"; transcript_id "uc001aea.2";
+chr1 hg19_knownGene exon 1233393 1233493 0.000000 - . gene_id "uc001aea.2"; transcript_id "uc001aea.2";
+chr1 hg19_knownGene CDS 1233750 1233801 0.000000 - 1 gene_id "uc001aea.2"; transcript_id "uc001aea.2";
+chr1 hg19_knownGene exon 1233750 1233801 0.000000 - . gene_id "uc001aea.2"; transcript_id "uc001aea.2";
+chr1 hg19_knownGene CDS 1233947 1234059 0.000000 - 0 gene_id "uc001aea.2"; transcript_id "uc001aea.2";
+chr1 hg19_knownGene exon 1233947 1234059 0.000000 - . gene_id "uc001aea.2"; transcript_id "uc001aea.2";
+chr1 hg19_knownGene CDS 1234725 1234736 0.000000 - 0 gene_id "uc001aea.2"; transcript_id "uc001aea.2";
+chr1 hg19_knownGene exon 1234725 1234736 0.000000 - . gene_id "uc001aea.2"; transcript_id "uc001aea.2";
+chr1 hg19_knownGene CDS 1235211 1235285 0.000000 - 0 gene_id "uc001aea.2"; transcript_id "uc001aea.2";
+chr1 hg19_knownGene exon 1235211 1235285 0.000000 - . gene_id "uc001aea.2"; transcript_id "uc001aea.2";
+chr1 hg19_knownGene CDS 1235353 1235448 0.000000 - 0 gene_id "uc001aea.2"; transcript_id "uc001aea.2";
+chr1 hg19_knownGene exon 1235353 1235448 0.000000 - . gene_id "uc001aea.2"; transcript_id "uc001aea.2";
+chr1 hg19_knownGene CDS 1235538 1235582 0.000000 - 0 gene_id "uc001aea.2"; transcript_id "uc001aea.2";
+chr1 hg19_knownGene exon 1235538 1235582 0.000000 - . gene_id "uc001aea.2"; transcript_id "uc001aea.2";
+chr1 hg19_knownGene CDS 1235889 1236072 0.000000 - 1 gene_id "uc001aea.2"; transcript_id "uc001aea.2";
+chr1 hg19_knownGene exon 1235889 1236072 0.000000 - . gene_id "uc001aea.2"; transcript_id "uc001aea.2";
+chr1 hg19_knownGene CDS 1237368 1237426 0.000000 - 0 gene_id "uc001aea.2"; transcript_id "uc001aea.2";
+chr1 hg19_knownGene exon 1237368 1237426 0.000000 - . gene_id "uc001aea.2"; transcript_id "uc001aea.2";
+chr1 hg19_knownGene CDS 1238302 1238355 0.000000 - 0 gene_id "uc001aea.2"; transcript_id "uc001aea.2";
+chr1 hg19_knownGene exon 1238302 1238355 0.000000 - . gene_id "uc001aea.2"; transcript_id "uc001aea.2";
+chr1 hg19_knownGene CDS 1238542 1238640 0.000000 - 0 gene_id "uc001aea.2"; transcript_id "uc001aea.2";
+chr1 hg19_knownGene start_codon 1238638 1238640 0.000000 - . gene_id "uc001aea.2"; transcript_id "uc001aea.2";
+chr1 hg19_knownGene exon 1238542 1238661 0.000000 - . gene_id "uc001aea.2"; transcript_id "uc001aea.2";
+chr1 hg19_knownGene exon 1239466 1241309 0.000000 - . gene_id "uc001aea.2"; transcript_id "uc001aea.2";
+chr1 hg19_knownGene CDS 1228944 1229088 0.000000 - 1 gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene exon 1227764 1229088 0.000000 - . gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene CDS 1229203 1229313 0.000000 - 1 gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene exon 1229203 1229313 0.000000 - . gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene CDS 1229470 1229579 0.000000 - 0 gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene exon 1229470 1229579 0.000000 - . gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene CDS 1229782 1230008 0.000000 - 2 gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene exon 1229782 1230008 0.000000 - . gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene CDS 1230098 1230196 0.000000 - 2 gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene exon 1230098 1230196 0.000000 - . gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene CDS 1230827 1230934 0.000000 - 2 gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene exon 1230827 1230934 0.000000 - . gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene CDS 1231116 1231318 0.000000 - 1 gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene exon 1231116 1231318 0.000000 - . gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene CDS 1231395 1231489 0.000000 - 0 gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene exon 1231395 1231489 0.000000 - . gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene CDS 1231591 1231660 0.000000 - 1 gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene exon 1231591 1231660 0.000000 - . gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene CDS 1231805 1232013 0.000000 - 0 gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene exon 1231805 1232013 0.000000 - . gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene CDS 1233202 1233313 0.000000 - 1 gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene exon 1233202 1233313 0.000000 - . gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene CDS 1233393 1233493 0.000000 - 0 gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene exon 1233393 1233493 0.000000 - . gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene CDS 1233750 1233801 0.000000 - 1 gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene exon 1233750 1233801 0.000000 - . gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene CDS 1233947 1234059 0.000000 - 0 gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene exon 1233947 1234059 0.000000 - . gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene CDS 1234725 1234736 0.000000 - 0 gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene exon 1234725 1234736 0.000000 - . gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene CDS 1235211 1235285 0.000000 - 0 gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene exon 1235211 1235285 0.000000 - . gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene CDS 1235353 1235448 0.000000 - 0 gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene exon 1235353 1235448 0.000000 - . gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene CDS 1235538 1235582 0.000000 - 0 gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene exon 1235538 1235582 0.000000 - . gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene CDS 1235889 1236072 0.000000 - 1 gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene exon 1235889 1236072 0.000000 - . gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene CDS 1237368 1237426 0.000000 - 0 gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene exon 1237368 1237426 0.000000 - . gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene CDS 1238302 1238355 0.000000 - 0 gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene exon 1238302 1238355 0.000000 - . gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene CDS 1238542 1238661 0.000000 - 0 gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene exon 1238542 1238661 0.000000 - . gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene CDS 1239466 1239523 0.000000 - 1 gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene exon 1239466 1239523 0.000000 - . gene_id "uc001aeb.2"; transcript_id "uc001aeb.2";
+chr1 hg19_knownGene CDS 1243149 1243195 0.000000 - 0 gene_id "uc001aeb.2"; transcrip
+
diff --git a/src/mergeBed/mergeBed.cpp b/src/mergeBed/mergeBed.cpp
index e140394585528ece3b7f22e6aba81c7f00cce049..ef234f576c2fcee2476376561cfa142ed48f3cc6 100755
--- a/src/mergeBed/mergeBed.cpp
+++ b/src/mergeBed/mergeBed.cpp
@@ -233,7 +233,7 @@ void BedMerge::MergeBedStranded() {
}
else {
- // was there an overlap befor the current entry broke it?
+ // was there an overlap before the current entry broke it?
if (OIP) {
if (this->numEntries) {
cout << bedList[prev].chrom << "\t" << minStart << "\t" << maxEnd << "\t" << mergeCount << "\t" << strands[s] << endl;
diff --git a/src/mergeBed/mergeMain.cpp b/src/mergeBed/mergeMain.cpp
index 38046d8f9f3f7ea0b8735996eac90bb3a9eb774f..6a6081c1548a0096fa233156ff52ffea96ce0591 100755
--- a/src/mergeBed/mergeMain.cpp
+++ b/src/mergeBed/mergeMain.cpp
@@ -122,7 +122,7 @@ void ShowHelp(void) {
cerr << "\t- By default, merging is done without respect to strand." << 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 << "\t- Note: \"1\" is reported if no merging occurred." << endl << endl;
cerr << " " << "-d\t" << "Maximum distance between features allowed for features to be merged." << endl;
diff --git a/src/utils/bedFile/bedFile.cpp b/src/utils/bedFile/bedFile.cpp
index 3c975f575c363944fe09a439bd4a25ec00cdacd0..40e6e13662d9e70424fbe3e32901e4bba134f301 100755
--- a/src/utils/bedFile/bedFile.cpp
+++ b/src/utils/bedFile/bedFile.cpp
@@ -475,33 +475,52 @@ bool BedFile::parseGffLine (BED &bed, const vector<string> &lineVector, int line
void BedFile::loadBedFileIntoMap() {
- // open the BED file for reading
- ifstream bed(bedFile.c_str(), ios::in);
- if ( !bed ) {
- cerr << "Error: The requested bed file (" <<bedFile << ") could not be opened. Exiting!" << endl;
- exit (1);
- }
-
- string bedLine;
+ string bedLine;
+ BED bedEntry;
int lineNum = 0;
vector<string> bedFields; // vector of strings for each column in BED file.
- bedFields.reserve(12); // reserve space for worst case (BED 6)
+ bedFields.reserve(12); // reserve space for worst case (BED 12)
+
+
+ // Case 1: Proper BED File.
+ if ( (this->bedFile != "") && (this->bedFile != "stdin") ) {
+
+ // open the BED file for reading
+ ifstream bed(bedFile.c_str(), ios::in);
+ if ( !bed ) {
+ cerr << "Error: The requested bed file (" <<bedFile << ") could not be opened. Exiting!" << endl;
+ exit (1);
+ }
+
+ while (getline(bed, bedLine)) {
+ lineNum++;
+
+ Tokenize(bedLine,bedFields);
- while (getline(bed, bedLine)) {
- lineNum++;
- BED bedEntry;
+ if (parseLine(bedEntry, bedFields, lineNum)) {
+ int bin = getBin(bedEntry.start, bedEntry.end);
+ bedEntry.count = 0;
+ bedEntry.minOverlapStart = INT_MAX;
+ this->bedMap[bedEntry.chrom][bin].push_back(bedEntry);
+ }
+ bedFields.clear();
+ }
+ }
+ else {
+ while (getline(cin, bedLine)) {
+ lineNum++;
- Tokenize(bedLine,bedFields);
+ Tokenize(bedLine,bedFields);
- if (parseLine(bedEntry, bedFields, lineNum)) {
- //this->reportBedNewLine(bedEntry);
- int bin = getBin(bedEntry.start, bedEntry.end);
- bedEntry.count = 0;
- bedEntry.minOverlapStart = INT_MAX;
- this->bedMap[bedEntry.chrom][bin].push_back(bedEntry);
+ if (parseLine(bedEntry, bedFields, lineNum)) {
+ int bin = getBin(bedEntry.start, bedEntry.end);
+ bedEntry.count = 0;
+ bedEntry.minOverlapStart = INT_MAX;
+ this->bedMap[bedEntry.chrom][bin].push_back(bedEntry);
+ }
+ bedFields.clear();
}
- bedFields.clear();
}
}
@@ -513,7 +532,7 @@ void BedFile::loadBedFileIntoMapNoBin() {
int lineNum = 0;
vector<string> bedFields; // vector of strings for each column in BED file.
- bedFields.reserve(12); // reserve space for worst case (BED 6)
+ bedFields.reserve(12); // reserve space for worst case (BED 12)
// Case 1: Proper BED File.
if ( (this->bedFile != "") && (this->bedFile != "stdin") ) {