diff --git a/bin/closestBed b/bin/closestBed
index d40f5ed0385a496d725414e187e900042fb6094f..ed7c3ab94574aba2f41ca76f7b31af31e2accafc 100755
Binary files a/bin/closestBed and b/bin/closestBed differ
diff --git a/bin/complementBed b/bin/complementBed
index c1a7c6654833eab43772c9ab45b876c00ab3c768..093f4d29ac91fff0d315d13f526512afcd3911b5 100755
Binary files a/bin/complementBed and b/bin/complementBed differ
diff --git a/bin/coverageBed b/bin/coverageBed
index dae26ad1341da08355f45f40a01a35e727ff30b2..882662a6be14bb8ed6f9ba44ba05953fe725ecd7 100755
Binary files a/bin/coverageBed and b/bin/coverageBed differ
diff --git a/bin/fastaFromBed b/bin/fastaFromBed
index 470987951012070135550a48b76eb18f631ed04f..3b68c5bb46d9e777366cfc53ad71bfa4dbb1c35e 100755
Binary files a/bin/fastaFromBed and b/bin/fastaFromBed differ
diff --git a/bin/genomeCoverageBed b/bin/genomeCoverageBed
index 2d9842ec848426c8eee531eae3f90230a55f34d6..c0ea6df851da538903ff8f10044cdf685890ff6b 100755
Binary files a/bin/genomeCoverageBed and b/bin/genomeCoverageBed differ
diff --git a/bin/intersectBed b/bin/intersectBed
index 9fc2522cfd56bd7eb6c416556811894cf82cee49..d467af1bf99a0d85bcd865c4dae617135e740e30 100755
Binary files a/bin/intersectBed and b/bin/intersectBed differ
diff --git a/bin/linksBed b/bin/linksBed
index beff05fa4612f5b1b7e8e564aef0ec52e143c7a6..db4a9a0f0bd424d4ce017957b0d42bec938089bb 100755
Binary files a/bin/linksBed and b/bin/linksBed differ
diff --git a/bin/mergeBed b/bin/mergeBed
index 31bfacd9569c7d588d2e245fe143c11a57ebc938..6905be49616be27ee0d9962b83c43f27a2db6bb4 100755
Binary files a/bin/mergeBed and b/bin/mergeBed differ
diff --git a/bin/peIntersectBed b/bin/peIntersectBed
index 27e1e0864b53d2bd44b973ba204a22eba4cb02be..25025e00675d6223fd762dda58148bedcb8bd5b7 100755
Binary files a/bin/peIntersectBed and b/bin/peIntersectBed differ
diff --git a/bin/sortBed b/bin/sortBed
index 2951603d77aa5514f93fd7ece20de40b00f5ad68..f337f32fabb09f7d18f6b7e4d2b0fb20d372f919 100755
Binary files a/bin/sortBed and b/bin/sortBed differ
diff --git a/bin/subtractBed b/bin/subtractBed
index 5e1658d43563f48d608b3d721344a3ae160ead84..ea04a337eb0908ca8b4ecff161e54cdb5f359803 100755
Binary files a/bin/subtractBed and b/bin/subtractBed differ
diff --git a/bin/windowBed b/bin/windowBed
index 7b4159aab992f275f926ef4d70a3ade5abe64e06..f3c83579ac7759b89d20d56578edcfec445273d8 100755
Binary files a/bin/windowBed and b/bin/windowBed differ
diff --git a/src/closestBed/closestMain.cpp b/src/closestBed/closestMain.cpp
index 4886a1883aeb6469d2fb6185e2898d358c6457c0..fad61ee2a709fe6d840e6bd9ff9b60da71c7f5dd 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 c6d58be61b888adf686cfaa09d970ff6ec044636..cc8f3bb64fd7a41c3ce1aac9203439f77fbad836 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 b7eac98026cf1d10eaea17aa74e14beb2b81497d..f3583d98f5852df8a6ba99dd63fe2d607a5ae8a2 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 59094e2d265ef631781e8693018800aa132cc12f..ea481513bc8aae666dde2f3c26a872e30c7b3746 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 e5bd2527962cae1a1ac5bc036cebb2c940e26007..0facc5e4976a410293c33f16a85afd9da920a38a 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 d31d338c7bfa4d9801cdea9f38e276917b379b80..a2cff2826a47d437400455f1f01a8419dd04749c 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 a6fe61b9eb6f415e6f1dbe8a4f33d537849973ae..5ca061e37a4eb292b873abd2a3286cbfb91e126d 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 a5383a3dacaa218708e08ca5f9f80d9a753fca56..311377cee84ae43a112d4940048e33ecda21919d 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 a9ecd37b5b69dc70f27b0ca2aebfb7e976ba3277..8c1e2910fc6e84fd54aef11e4709816f4eef8e99 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 1d46d937929d572d1db7c315e7b7ba061122a3cd..65264935ffe31728e1aa0de75f809fafd7222ec1 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 22c9db3c158abd494b2fcad0782a52bc6d0f6925..6292479412a83f7ef3f7f9b35eb5cb267595db84 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 eeb960c0bb0d62c15b0ace820886e6dc84fb229a..f46c5df3f8559245bd4c66fbff21a5b64ee341b4 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 ddf56656c8205f45567cd2d7a9f855a26dccbc04..8978cb79cee8b9f45bed83ed54d34be6ee88835f 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;
}
}