diff --git a/bin/mergeBed b/bin/mergeBed
index a2790b4ca21800d19415fce6134d1849bfdb7a0b..b3484dbeaa4febced154c05966ba8f6433f48e01 100755
Binary files a/bin/mergeBed and b/bin/mergeBed differ
diff --git a/obj/bedFile.o b/obj/bedFile.o
index 3cc0cd76f33b7c5053af7ddcd7db5d09c610f91e..1e7a0d65d39c05d154bd0bce50726c041381f3cf 100644
Binary files a/obj/bedFile.o and b/obj/bedFile.o differ
diff --git a/obj/mergeMain.o b/obj/mergeMain.o
index 568d6641a74d95a061eef997d2ffc723b4a94d50..d9f68d96d6b348063dcddbb1502e8e52733de68f 100644
Binary files a/obj/mergeMain.o and b/obj/mergeMain.o differ
diff --git a/src/closestBed/closestMain.cpp b/src/closestBed/closestMain.cpp
index e8698eca5cbf89f337c212d2c1444d23dcc09465..f4efd748d75f5387e7f386fdfff0c90562fecce9 100755
--- a/src/closestBed/closestMain.cpp
+++ b/src/closestBed/closestMain.cpp
@@ -102,11 +102,10 @@ 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 << endl << "PROGRAM: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl << endl;
+
+ cerr << "AUTHOR: Aaron Quinlan (aaronquinlan@gmail.com)" << endl << endl ;
+
cerr << "SUMMARY: For each feature in BED A, finds the closest " << endl;
cerr << "\t feature (upstream or downstream) in BED B." << endl << endl;
diff --git a/src/intersectBed/intersectMain.cpp b/src/intersectBed/intersectMain.cpp
index 64e5caef33e05dcea733bbed6cad819017307095..acb5f2d30406b240adbcda7fca2d50e1cccef3a7 100755
--- a/src/intersectBed/intersectMain.cpp
+++ b/src/intersectBed/intersectMain.cpp
@@ -151,11 +151,10 @@ 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 << endl << "PROGRAM: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl << endl;
+
+ cerr << "AUTHOR: Aaron Quinlan (aaronquinlan@gmail.com)" << endl << endl ;
+
cerr << "SUMMARY: Report overlaps between a.bed and b.bed." << endl << endl;
cerr << "USAGE: " << PROGRAM_NAME << " [OPTIONS] -a <a.bed> -b <b.bed>" << endl << endl;
@@ -176,7 +175,8 @@ void ShowHelp(void) {
cerr << "\t- Similar to \"grep -v.\"" << endl << endl;
cerr << " " << "-f\t" << "Minimum overlap required as a fraction of A." << endl;
- cerr << "\t- Default is 1E-9 (i.e., 1bp)." << endl << endl;
+ cerr << "\t- Default is 1E-9 (i.e., 1bp)." << endl;
+ cerr << "\t- FLOAT (e.g. 0.50)" << endl << endl;
cerr << " " << "-r\t" << "Require that the fraction overlap be reciprocal for A and B." << endl;
cerr << "\t- In other words, if -f is 0.90 and -r is used, this requires" << endl;
diff --git a/src/mergeBed/a.bed b/src/mergeBed/a.bed
new file mode 100644
index 0000000000000000000000000000000000000000..c2a8b2733b0e0196c294ac5f594b0725db4ba9b8
--- /dev/null
+++ b/src/mergeBed/a.bed
@@ -0,0 +1,2 @@
+chr1 10 20 a
+chr1 15 25 b
diff --git a/src/mergeBed/mergeBed.cpp b/src/mergeBed/mergeBed.cpp
index 5411ec67d5b2019cf36fa591b3194b02d36a449a..e140394585528ece3b7f22e6aba81c7f00cce049 100755
--- a/src/mergeBed/mergeBed.cpp
+++ b/src/mergeBed/mergeBed.cpp
@@ -1,12 +1,14 @@
-//
-// mergeBed.cpp
-// BEDTools
-//
-// Created by Aaron Quinlan Spring 2009.
-// Copyright 2009 Aaron Quinlan. All rights reserved.
-//
-// Summary: Combines overlapping BED entries into a single entry.
-//
+/*****************************************************************************
+ mergeBed.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 "mergeBed.h"
@@ -22,7 +24,6 @@ BedMerge::BedMerge(string &bedFile, bool &numEntries, int &maxDistance, bool &fo
this->reportNames = reportNames;
this->bed = new BedFile(bedFile);
-
}
diff --git a/src/mergeBed/mergeBed.h b/src/mergeBed/mergeBed.h
index c3f1a8caf1a298b37f7a33d94ae4264b1e0f89ac..d6330985e97bc392d67c295407989ce2ed3fbd9d 100755
--- a/src/mergeBed/mergeBed.h
+++ b/src/mergeBed/mergeBed.h
@@ -1,3 +1,14 @@
+/*****************************************************************************
+ mergeBed.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.
+******************************************************************************/
#include "bedFile.h"
#include <vector>
#include <algorithm>
diff --git a/src/mergeBed/mergeMain.cpp b/src/mergeBed/mergeMain.cpp
index 2ea6f81183adccd66694466ba82ade8f14aaea28..38046d8f9f3f7ea0b8735996eac90bb3a9eb774f 100755
--- a/src/mergeBed/mergeMain.cpp
+++ b/src/mergeBed/mergeMain.cpp
@@ -1,3 +1,14 @@
+/*****************************************************************************
+ mergeMain.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 "mergeBed.h"
#include "version.h"
@@ -64,7 +75,7 @@ int main(int argc, char* argv[]) {
else if (PARAMETER_CHECK("-s", 2, parameterLength)) {
forceStrand = true;
}
- else if (PARAMETER_CHECK("-names", 6, parameterLength)) {
+ else if (PARAMETER_CHECK("-nms", 4, parameterLength)) {
reportNames = true;
}
else {
@@ -97,25 +108,29 @@ 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: Merges overlapping bed entries into a single interval." << endl << endl;
+ cerr << endl << "PROGRAM: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl << endl;
+
+ cerr << "AUTHOR: Aaron Quinlan (aaronquinlan@gmail.com)" << endl << endl ;
+
+ cerr << "SUMMARY: Merges overlapping BED entries into a single interval." << endl << endl;
- cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <input.bed>" << endl << endl;
+ cerr << "USAGE: " << PROGRAM_NAME << " [OPTIONS] -i <input.bed>" << endl << endl;
cerr << "OPTIONS: " << endl;
- cerr << "\t" << "-s\t\t" << "Force strandedness. Only report hits in B that overlap A on the same strand." << endl << "\t\t\tBy default, overlaps are reported without respect to strand." << endl << endl;
- cerr << "\t" << "-n\t\t" << "Report the number of BED entries that were merged. (=1 if no merging occured)" << endl << endl;
- cerr << "\t" << "-d\t\t" << "Maximum distance between features allowed for features to be merged. (Default=0)" << endl << endl;
- cerr << "\t" << "-names\t\t" << "Report the names of the merged features separated by semicolons." << endl << endl;
-
+ cerr << " " << "-s\t" << "Force strandedness. That is, only merge features" << endl;
+ cerr << "\tthat are the same strand." << endl;
+ cerr << "\t- By default, merging is done without respect to strand." << endl << endl;
- cerr << "NOTES: " << endl;
- cerr << "\t" << "-i stdin\t" << "Allows BED file A to be read from stdin. E.g.: cat a.bed | mergeBed -a stdin -b B.bed" << endl << endl;
- cerr << "\t***Only tab-delimited BED3 - BED6 formats allowed.***"<< 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 << " " << "-d\t" << "Maximum distance between features allowed for features to be merged." << endl;
+ cerr << "\t- Def. 0. That is, overlapping and/or book-ended features are merged." << endl;
+ cerr << "\t- INTEGER" << endl << endl;
+
+ cerr << " " << "-nms\t" << "Report the names of the merged features separated by semicolons." << endl << endl;
+
// end the program here
exit(1);
diff --git a/src/subtractBed/subtractMain.cpp b/src/subtractBed/subtractMain.cpp
index 592a78c8b158bf58c5c33d136eb7039b3a8a5d72..36b43c450f09c9c3b8214a3c8dfc3d8f241fdb14 100755
--- a/src/subtractBed/subtractMain.cpp
+++ b/src/subtractBed/subtractMain.cpp
@@ -107,11 +107,10 @@ 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 << endl << "PROGRAM: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl << endl;
+
+ cerr << "AUTHOR: Aaron Quinlan (aaronquinlan@gmail.com)" << endl << endl ;
+
cerr << "SUMMARY: Removes the portion(s) of an interval that is overlapped" << endl;
cerr << "\t by another feature(s)." << endl << endl;
@@ -119,7 +118,8 @@ void ShowHelp(void) {
cerr << "OPTIONS: " << endl;
cerr << " " << "-f\t" << "Minimum overlap required as a fraction of A." << endl;
- cerr << "\t- Default is 1E-9 (i.e., 1bp)." << endl << endl;
+ cerr << "\t- Default is 1E-9 (i.e., 1bp)." << endl;
+ cerr << "\t- FLOAT (e.g. 0.50)" << endl << endl;
cerr << " " << "-s\t" << "Force strandedness. That is, only report hits in B that" << endl;
cerr << "\toverlap A on the same strand." << endl;
diff --git a/src/utils/bedFile/bedFile.cpp b/src/utils/bedFile/bedFile.cpp
index e4ce797721cf03e70b16720cd80bcf9be45fe905..3c975f575c363944fe09a439bd4a25ec00cdacd0 100755
--- a/src/utils/bedFile/bedFile.cpp
+++ b/src/utils/bedFile/bedFile.cpp
@@ -545,20 +545,19 @@ void BedFile::loadBedFileIntoMapNoBin() {
}
// Case 2: STDIN.
else {
-
+
while (getline(cin, bedLine)) {
if ((bedLine.find("track") != string::npos) || (bedLine.find("browser") != string::npos)) {
continue;
}
else {
- vector<string> bedFields;
Tokenize(bedLine,bedFields);
-
lineNum++;
if (parseLine(bedEntry, bedFields, lineNum)) {
bedEntry.count = 0;
+ bedEntry.minOverlapStart = INT_MAX;
this->bedMapNoBin[bedEntry.chrom].push_back(bedEntry);
}
bedFields.clear();
diff --git a/src/windowBed/windowMain.cpp b/src/windowBed/windowMain.cpp
index fd2641d2e5141e6a06b0d4a2bf4210ff6f1dfa64..9099e91beb71b1920c4cbedb1b3a15d3a6783e47 100755
--- a/src/windowBed/windowMain.cpp
+++ b/src/windowBed/windowMain.cpp
@@ -162,11 +162,10 @@ 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 << endl << "PROGRAM: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl << endl;
+
+ cerr << "AUTHOR: Aaron Quinlan (aaronquinlan@gmail.com)" << endl << endl ;
+
cerr << "SUMMARY: Examines a \"window\" around each feature in A and" << endl;
cerr << "\t reports all features in B that overlap the window. For each" << endl;
cerr << "\t overlap the entire entry in A and B are reported." << endl << endl;
@@ -177,17 +176,20 @@ void ShowHelp(void) {
cerr << " " << "-w\t" << "Base pairs added upstream and downstream of each entry" << endl;
cerr << "\tin A when searching for overlaps in B." << endl;
cerr << "\t- Creates symterical \"windows\" around A." << endl;
- cerr << "\t- Default is 1000 bp." << endl << endl;
-
+ cerr << "\t- Default is 1000 bp." << endl;
+ cerr << "\t- INTEGER" << endl << endl;
+
cerr << " " << "-l\t" << "Base pairs added upstream (left of) of each entry" << endl;
cerr << "\tin A when searching for overlaps in B." << endl;
cerr << "\t- Allows one to define assymterical \"windows\"." << endl;
- cerr << "\t- Default is 1000 bp." << endl << endl;
+ cerr << "\t- Default is 1000 bp." << endl;
+ cerr << "\t- INTEGER" << endl << endl;
cerr << " " << "-r\t" << "Base pairs added downstream (right of) of each entry" << endl;
cerr << "\tin A when searching for overlaps in B." << endl;
cerr << "\t- Allows one to define assymterical \"windows\"." << endl;
- cerr << "\t- Default is 1000 bp." << endl << endl;
+ cerr << "\t- Default is 1000 bp." << endl;
+ cerr << "\t- INTEGER" << endl << endl;
cerr << " " << "-sw\t" << "Define -l and -r based on strand. For example if used, -l 500" << endl;