From 34bb6987b238aa9d1ca3e8fa7ca52cc6907e026d Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Tue, 12 May 2009 15:44:11 -0400
Subject: [PATCH] BEDTools Public Release 2.0
---
bin/closestBed | Bin 78336 -> 78336 bytes
bin/complementBed | Bin 74896 -> 74896 bytes
bin/coverageBed | Bin 74168 -> 74168 bytes
bin/fastaFromBed | Bin 79348 -> 79348 bytes
bin/genomeCoverageBed | Bin 94712 -> 94712 bytes
bin/intersectBed | Bin 82324 -> 82324 bytes
bin/linksBed | Bin 78776 -> 78776 bytes
bin/mergeBed | Bin 77932 -> 77932 bytes
bin/peIntersectBed | Bin 91120 -> 91120 bytes
bin/sortBed | Bin 70332 -> 70332 bytes
bin/subtractBed | Bin 73936 -> 73936 bytes
bin/windowBed | Bin 73944 -> 73944 bytes
src/closestBed/closestMain.cpp | 4 ++--
src/complementBed/complementBed.cpp | 1 -
src/complementBed/complementMain.cpp | 5 ++---
src/coverageBed/coverageMain.cpp | 4 ++--
src/fastaFromBed/fastaFromBedMain.cpp | 4 ++--
src/genomeCoverageBed/genomeCoverageMain.cpp | 5 ++---
src/intersectBed/intersectMain.cpp | 4 ++--
src/linksBed/linksMain.cpp | 5 ++---
src/mergeBed/mergeMain.cpp | 5 ++---
src/peIntersectBed/peIntersectMain.cpp | 4 ++--
src/sortBed/sortMain.cpp | 5 ++---
src/subtractBed/subtractMain.cpp | 4 ++--
src/windowBed/windowMain.cpp | 4 ++--
25 files changed, 24 insertions(+), 30 deletions(-)
diff --git a/bin/closestBed b/bin/closestBed
index d40f5ed0385a496d725414e187e900042fb6094f..ed7c3ab94574aba2f41ca76f7b31af31e2accafc 100755
GIT binary patch
delta 20
ccmZp8!qV`BWy1zmM&{;?tlKxTGWzQP09YRfTmS$7
delta 20
ccmZp8!qV`BWy1zmMyBSCtlKxTGWzQP09X|VTL1t6
diff --git a/bin/complementBed b/bin/complementBed
index c1a7c6654833eab43772c9ab45b876c00ab3c768..093f4d29ac91fff0d315d13f526512afcd3911b5 100755
GIT binary patch
delta 20
bcmbPml4Zh4mJJrHjLglJtlKSF8N=lPN|6QG
delta 20
bcmbPml4Zh4mJJrHj7-gztlKSF8N=lPN{0p5
diff --git a/bin/coverageBed b/bin/coverageBed
index dae26ad1341da08355f45f40a01a35e727ff30b2..882662a6be14bb8ed6f9ba44ba05953fe725ecd7 100755
GIT binary patch
delta 20
bcmdmSm}SRdmJK<qjLglstlM*08NFoyRI~=F
delta 20
bcmdmSm}SRdmJK<qj7-hBtlM*08NFoyRH_E4
diff --git a/bin/fastaFromBed b/bin/fastaFromBed
index 470987951012070135550a48b76eb18f631ed04f..3b68c5bb46d9e777366cfc53ad71bfa4dbb1c35e 100755
GIT binary patch
delta 20
bcmezJn&r!DmJK<qjLglstlM*08QTp2V`K-y
delta 20
bcmezJn&r!DmJK<qj7-hBtlM*08QTp2V_FBn
diff --git a/bin/genomeCoverageBed b/bin/genomeCoverageBed
index 2d9842ec848426c8eee531eae3f90230a55f34d6..c0ea6df851da538903ff8f10044cdf685890ff6b 100755
GIT binary patch
delta 20
ccmezInDxhF)(sn28JU|mvTonV%IKa00BNNNga7~l
delta 20
ccmezInDxhF)(sn28JU_lvTonV%IKa00BM^Dg8%>k
diff --git a/bin/intersectBed b/bin/intersectBed
index 9fc2522cfd56bd7eb6c416556811894cf82cee49..d467af1bf99a0d85bcd865c4dae617135e740e30 100755
GIT binary patch
delta 20
bcmbQz%sQo+bwds-BXe^u>-Jn$Ms*tiM!5yx
delta 20
bcmbQz%sQo+bwds-BU5uO>-Jn$Ms*tiMz00m
diff --git a/bin/linksBed b/bin/linksBed
index beff05fa4612f5b1b7e8e564aef0ec52e143c7a6..db4a9a0f0bd424d4ce017957b0d42bec938089bb 100755
GIT binary patch
delta 20
bcmdn-oMp#zmJK<qjLglstlM*08NKxYS+WNN
delta 20
bcmdn-oMp#zmJK<qj7-hBtlM*08NKxYS*QmC
diff --git a/bin/mergeBed b/bin/mergeBed
index 31bfacd9569c7d588d2e245fe143c11a57ebc938..6905be49616be27ee0d9962b83c43f27a2db6bb4 100755
GIT binary patch
delta 20
ccmaF!faT2tmJK<qjLglstlM*08UJem0AZyF4gdfE
delta 20
ccmaF!faT2tmJK<qj7-hBtlM*08UJem0AZU54FCWD
diff --git a/bin/peIntersectBed b/bin/peIntersectBed
index 27e1e0864b53d2bd44b973ba204a22eba4cb02be..25025e00675d6223fd762dda58148bedcb8bd5b7 100755
GIT binary patch
delta 20
bcmexxob|(T)(ttVjLglstlM*08Jpt(UMmNl
delta 20
bcmexxob|(T)(ttVj7-hBtlM*08Jpt(ULgma
diff --git a/bin/sortBed b/bin/sortBed
index 2951603d77aa5514f93fd7ece20de40b00f5ad68..f337f32fabb09f7d18f6b7e4d2b0fb20d372f919 100755
GIT binary patch
delta 20
bcmdn9lx5FSmJK<qjLglstlM*08U1+yQ6~m#
delta 20
bcmdn9lx5FSmJK<qj7-hBtlM*08U1+yQ5^<q
diff --git a/bin/subtractBed b/bin/subtractBed
index 5e1658d43563f48d608b3d721344a3ae160ead84..ea04a337eb0908ca8b4ecff161e54cdb5f359803 100755
GIT binary patch
delta 20
ccmca`kmbTbmJJ(N8JU|mvTonV$|x@l0A6(mbpQYW
delta 20
ccmca`kmbTbmJJ(N8JU_lvTonV$|x@l0A6bcbN~PV
diff --git a/bin/windowBed b/bin/windowBed
index 7b4159aab992f275f926ef4d70a3ade5abe64e06..f3c83579ac7759b89d20d56578edcfec445273d8 100755
GIT binary patch
delta 20
ccmca{kmbffmJJ(N8JU|mvTonV%BU_40AH;KjQ{`u
delta 20
ccmca{kmbffmJJ(N8JU_lvTonV%BU_40AHgAi~s-t
diff --git a/src/closestBed/closestMain.cpp b/src/closestBed/closestMain.cpp
index 4886a188..fad61ee2 100755
--- a/src/closestBed/closestMain.cpp
+++ b/src/closestBed/closestMain.cpp
@@ -31,8 +31,8 @@ int main(int argc, char* argv[]) {
for(int i = 1; i < argc; i++) {
int parameterLength = (int)strlen(argv[i]);
- if(PARAMETER_CHECK("-h", 2, parameterLength) ||
- PARAMETER_CHECK("--help", 5, parameterLength)) {
+ if( (PARAMETER_CHECK("-h", 2, parameterLength)) ||
+ (PARAMETER_CHECK("--help", 5, parameterLength))) {
showHelp = true;
}
}
diff --git a/src/complementBed/complementBed.cpp b/src/complementBed/complementBed.cpp
index c6d58be6..cc8f3bb6 100755
--- a/src/complementBed/complementBed.cpp
+++ b/src/complementBed/complementBed.cpp
@@ -7,7 +7,6 @@
//
// Summary: Return the intervals NOT spanned by a BED file.
//
-
#include "lineFileUtilities.h"
#include "complementBed.h"
diff --git a/src/complementBed/complementMain.cpp b/src/complementBed/complementMain.cpp
index b7eac980..f3583d98 100755
--- a/src/complementBed/complementMain.cpp
+++ b/src/complementBed/complementMain.cpp
@@ -1,4 +1,3 @@
-#include <iostream>
#include "complementBed.h"
#include "version.h"
@@ -32,8 +31,8 @@ int main(int argc, char* argv[]) {
for(int i = 1; i < argc; i++) {
int parameterLength = (int)strlen(argv[i]);
- if(PARAMETER_CHECK("-h", 2, parameterLength) ||
- PARAMETER_CHECK("--help", 5, parameterLength)) {
+ if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
+ (PARAMETER_CHECK("--help", 5, parameterLength))) {
showHelp = true;
}
}
diff --git a/src/coverageBed/coverageMain.cpp b/src/coverageBed/coverageMain.cpp
index 59094e2d..ea481513 100755
--- a/src/coverageBed/coverageMain.cpp
+++ b/src/coverageBed/coverageMain.cpp
@@ -30,8 +30,8 @@ int main(int argc, char* argv[]) {
for(int i = 1; i < argc; i++) {
int parameterLength = (int)strlen(argv[i]);
- if(PARAMETER_CHECK("-h", 2, parameterLength) ||
- PARAMETER_CHECK("--help", 5, parameterLength)) {
+ if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
+ (PARAMETER_CHECK("--help", 5, parameterLength))) {
showHelp = true;
}
}
diff --git a/src/fastaFromBed/fastaFromBedMain.cpp b/src/fastaFromBed/fastaFromBedMain.cpp
index e5bd2527..0facc5e4 100755
--- a/src/fastaFromBed/fastaFromBedMain.cpp
+++ b/src/fastaFromBed/fastaFromBedMain.cpp
@@ -37,8 +37,8 @@ int main(int argc, char* argv[]) {
for(int i = 1; i < argc; i++) {
int parameterLength = (int)strlen(argv[i]);
- if(PARAMETER_CHECK("-h", 2, parameterLength) ||
- PARAMETER_CHECK("--help", 5, parameterLength)) {
+ if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
+ (PARAMETER_CHECK("--help", 5, parameterLength))) {
showHelp = true;
}
}
diff --git a/src/genomeCoverageBed/genomeCoverageMain.cpp b/src/genomeCoverageBed/genomeCoverageMain.cpp
index d31d338c..a2cff282 100755
--- a/src/genomeCoverageBed/genomeCoverageMain.cpp
+++ b/src/genomeCoverageBed/genomeCoverageMain.cpp
@@ -1,4 +1,3 @@
-#include <iostream>
#include "genomeCoverageBed.h"
#include "version.h"
@@ -35,8 +34,8 @@ int main(int argc, char* argv[]) {
for(int i = 1; i < argc; i++) {
int parameterLength = (int)strlen(argv[i]);
- if(PARAMETER_CHECK("-h", 2, parameterLength) ||
- PARAMETER_CHECK("--help", 5, parameterLength)) {
+ if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
+ (PARAMETER_CHECK("--help", 5, parameterLength))) {
showHelp = true;
}
}
diff --git a/src/intersectBed/intersectMain.cpp b/src/intersectBed/intersectMain.cpp
index a6fe61b9..5ca061e3 100755
--- a/src/intersectBed/intersectMain.cpp
+++ b/src/intersectBed/intersectMain.cpp
@@ -41,8 +41,8 @@ int main(int argc, char* argv[]) {
for(int i = 1; i < argc; i++) {
int parameterLength = (int)strlen(argv[i]);
- if(PARAMETER_CHECK("-h", 2, parameterLength) ||
- PARAMETER_CHECK("--help", 5, parameterLength)) {
+ if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
+ (PARAMETER_CHECK("--help", 5, parameterLength))) {
showHelp = true;
}
}
diff --git a/src/linksBed/linksMain.cpp b/src/linksBed/linksMain.cpp
index a5383a3d..311377ce 100755
--- a/src/linksBed/linksMain.cpp
+++ b/src/linksBed/linksMain.cpp
@@ -1,4 +1,3 @@
-#include <iostream>
#include "linksBed.h"
#include "version.h"
@@ -37,8 +36,8 @@ int main(int argc, char* argv[]) {
for(int i = 1; i < argc; i++) {
int parameterLength = (int)strlen(argv[i]);
- if(PARAMETER_CHECK("-h", 2, parameterLength) ||
- PARAMETER_CHECK("--help", 5, parameterLength)) {
+ if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
+ (PARAMETER_CHECK("--help", 5, parameterLength))) {
showHelp = true;
}
}
diff --git a/src/mergeBed/mergeMain.cpp b/src/mergeBed/mergeMain.cpp
index a9ecd37b..8c1e2910 100755
--- a/src/mergeBed/mergeMain.cpp
+++ b/src/mergeBed/mergeMain.cpp
@@ -1,4 +1,3 @@
-#include <iostream>
#include "mergeBed.h"
#include "version.h"
@@ -35,8 +34,8 @@ int main(int argc, char* argv[]) {
for(int i = 1; i < argc; i++) {
int parameterLength = (int)strlen(argv[i]);
- if(PARAMETER_CHECK("-h", 2, parameterLength) ||
- PARAMETER_CHECK("--help", 5, parameterLength)) {
+ if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
+ (PARAMETER_CHECK("--help", 5, parameterLength))) {
showHelp = true;
}
}
diff --git a/src/peIntersectBed/peIntersectMain.cpp b/src/peIntersectBed/peIntersectMain.cpp
index 1d46d937..65264935 100755
--- a/src/peIntersectBed/peIntersectMain.cpp
+++ b/src/peIntersectBed/peIntersectMain.cpp
@@ -37,8 +37,8 @@ int main(int argc, char* argv[]) {
for(int i = 1; i < argc; i++) {
int parameterLength = (int)strlen(argv[i]);
- if(PARAMETER_CHECK("-h", 2, parameterLength) ||
- PARAMETER_CHECK("--help", 5, parameterLength)) {
+ if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
+ (PARAMETER_CHECK("--help", 5, parameterLength))) {
showHelp = true;
}
}
diff --git a/src/sortBed/sortMain.cpp b/src/sortBed/sortMain.cpp
index 22c9db3c..62924794 100755
--- a/src/sortBed/sortMain.cpp
+++ b/src/sortBed/sortMain.cpp
@@ -1,4 +1,3 @@
-#include <iostream>
#include "sortBed.h"
#include "version.h"
@@ -34,8 +33,8 @@ int main(int argc, char* argv[]) {
for(int i = 1; i < argc; i++) {
int parameterLength = (int)strlen(argv[i]);
- if(PARAMETER_CHECK("-h", 2, parameterLength) ||
- PARAMETER_CHECK("--help", 5, parameterLength)) {
+ if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
+ (PARAMETER_CHECK("--help", 5, parameterLength))) {
showHelp = true;
}
}
diff --git a/src/subtractBed/subtractMain.cpp b/src/subtractBed/subtractMain.cpp
index eeb960c0..f46c5df3 100755
--- a/src/subtractBed/subtractMain.cpp
+++ b/src/subtractBed/subtractMain.cpp
@@ -36,8 +36,8 @@ int main(int argc, char* argv[]) {
for(int i = 1; i < argc; i++) {
int parameterLength = (int)strlen(argv[i]);
- if(PARAMETER_CHECK("-h", 2, parameterLength) ||
- PARAMETER_CHECK("--help", 5, parameterLength)) {
+ if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
+ (PARAMETER_CHECK("--help", 5, parameterLength))) {
showHelp = true;
}
}
diff --git a/src/windowBed/windowMain.cpp b/src/windowBed/windowMain.cpp
index ddf56656..8978cb79 100755
--- a/src/windowBed/windowMain.cpp
+++ b/src/windowBed/windowMain.cpp
@@ -42,8 +42,8 @@ int main(int argc, char* argv[]) {
for(int i = 1; i < argc; i++) {
int parameterLength = (int)strlen(argv[i]);
- if(PARAMETER_CHECK("-h", 2, parameterLength) ||
- PARAMETER_CHECK("--help", 5, parameterLength)) {
+ if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
+ (PARAMETER_CHECK("--help", 5, parameterLength))) {
showHelp = true;
}
}
--
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