diff --git a/bin/closestBed b/bin/closestBed
index bd91ece0aaeae7e8b82766e049ae06542fc79cd4..b6f130a4007631f341a4c0d2a2be96ccf4c42ca1 100755
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diff --git a/bin/complementBed b/bin/complementBed
index 1e9c95905d1d5f74b4afbd7028e0124a76e6b464..7f9660434cbfc096ea4f3869899d5ae1eb3bb8a0 100755
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diff --git a/bin/coverageBed b/bin/coverageBed
index 4a73789469585815c7a1091503e18e48558a866d..b25063590a9f8e98891baaa369212ea49c6698c6 100755
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diff --git a/bin/fastaFromBed b/bin/fastaFromBed
index 7a58ed3e7e57b6726e1f109a30daae25bb4bc3e5..b9754b86f8f9d62b6ddb49738fa5f3fd4044df8d 100755
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diff --git a/bin/genomeCoverageBed b/bin/genomeCoverageBed
index 04df3a4868f6cf3ed3afd032a1134e3610bb7620..4d5da090724acb856bef0da8554688eda1ae70e3 100755
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diff --git a/bin/intersectBed b/bin/intersectBed
index e62cfa640c049b71d213f6b321e949b1feb4dca0..70b5b77365b9a18ef71b9b95dc9d27ca5b4fe0ae 100755
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diff --git a/bin/linksBed b/bin/linksBed
index 157888c6681fc9f251f3b2e0723061f4490931cd..4fb13780e2ffeec5000fb9aebe2561da53a90933 100755
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diff --git a/bin/mergeBed b/bin/mergeBed
index 585d99d1dfa3f36fe1835c70d06df562d6f935a2..7bb5d5baf3f89c1be37237823adccfb0aff7ef94 100755
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diff --git a/bin/peIntersectBed b/bin/peIntersectBed
index 734da80eaa38e36c72882a4b0ead9c224c9e32c2..1dbb172b530ee1a6d9391481e6425223de8ce95a 100755
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diff --git a/bin/sortBed b/bin/sortBed
index 8b97b18da11a5785a0a0eca09a4890434eaf5fdf..40bd199f11ac6b4dd7879dcf06405569bb927d17 100755
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diff --git a/bin/subtractBed b/bin/subtractBed
index 44ec9dc8f3976271b3e09b25f778a301af074abb..4150a0fbfabc4ab984b041f6571452e66345b2e8 100755
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diff --git a/bin/windowBed b/bin/windowBed
index bf765cbc3c0201df7ff67d57b09a5e8d7c1d1c5b..393bfde9d5382d854302a584a4c65e45297bc9f7 100755
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diff --git a/obj/closestMain.o b/obj/closestMain.o
index 3792134b0b6cb3f049e2ed28ae5a4b625ae6db95..5bebdbf4f54b2ed9488125ed855b40497bffedae 100644
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diff --git a/obj/complementMain.o b/obj/complementMain.o
index de9a4318a1c4f5b386e4ab6da287a10dcde3eaa3..bb5e27263b5622dab1157e41d800ad8f04a75fb4 100644
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diff --git a/obj/coverageMain.o b/obj/coverageMain.o
index d530e5617bd80c5d885f736361ab070b03e38f22..9028015345753e3503cfe5860449c48111912be7 100644
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diff --git a/obj/fastaFromBedMain.o b/obj/fastaFromBedMain.o
index 0fac91fbd0202ca7ad3cb884d9149c6dbcad9463..43cbf9a282fb845a86d9c00b50d507b8207adfe8 100644
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diff --git a/obj/genomeCoverageMain.o b/obj/genomeCoverageMain.o
index 816dda1684f2d1103c6d79bda0df559786162faa..6de45c59eaba1884a89953057a94203b22d09dab 100644
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diff --git a/obj/intersectMain.o b/obj/intersectMain.o
index 0b7a9a29bd1f706d344f36614abb092c012567f4..a58d3391f48595544ed0e29a51851122549e3ad4 100644
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diff --git a/obj/linksMain.o b/obj/linksMain.o
index 0508c0ea0ea8d0a6bd0afd07bbbb4677a6c23356..3813eb2d92da814a16806f6995275e907fc2611b 100644
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diff --git a/obj/mergeMain.o b/obj/mergeMain.o
index ebdcabbc9273c4b941240c1c5f8f45932126b9d8..4eb54f446d0ab4ce2a48b813550e53a400180639 100644
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diff --git a/obj/peIntersectMain.o b/obj/peIntersectMain.o
index e01eafb05341bb1acda0a3f503775066dbd91305..e36b4f45f2216f29acbd535378b6bd6f0870ee81 100644
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diff --git a/obj/sortMain.o b/obj/sortMain.o
index 89d8509f567c3855d50dc015bacf10107297e4bc..1a8c92443a80fb6fa8123095771005d6df8c8a13 100644
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diff --git a/obj/subtractBed.o b/obj/subtractBed.o
index 4463d05bc3118c0f403703856cf83ca344af35b9..bf06bf9a21591b9514b0219ffa57445c66c532b9 100644
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diff --git a/obj/subtractMain.o b/obj/subtractMain.o
index c13b719ecf58f1ccdcdbba55bbed5c3ad250adfa..d682273ad7d94fdd6a13cbab4d40e48375fcb530 100644
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diff --git a/obj/windowMain.o b/obj/windowMain.o
index 6938940b3676bdc3f6ecd82f07aca1b088ca7b8e..a320a63363e595182c1020c9e09f2ff28976805b 100644
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diff --git a/src/genomeCoverageBed/genomeCoverageMain.cpp b/src/genomeCoverageBed/genomeCoverageMain.cpp
index ab216062015c09a51c172995dc58f7d9277240d4..305a4ff76489faa55b3db60fc58932f95449eeb1 100755
--- a/src/genomeCoverageBed/genomeCoverageMain.cpp
+++ b/src/genomeCoverageBed/genomeCoverageMain.cpp
@@ -100,7 +100,8 @@ void ShowHelp(void) {
 	cerr << " Hall Laboratory, University of Virginia" << endl;
 	cerr << "===============================================" << endl << endl;
 	cerr << "Description: Compute the coverage of a BED (-i) file on genome (-g) file." << endl << endl;
-	cerr << "***NOTE: Only BED3 - BED6 formats allowed.***"<< endl << endl;
+	cerr << "***NOTE: Only BED3 - BED6 formats allowed.***"<< endl;
+	cerr << "***NOTE: Input BED file must be grouped by chromosome.  A simple UNIX sort will suffice.***"<< endl << endl;
 
 	cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -g <genome> -i <bed>" << endl << endl;
 	
@@ -114,7 +115,6 @@ void ShowHelp(void) {
 	cerr << "\tchr2\t181748087" << endl;
 	cerr << "\t..." << endl;
 	cerr << "\tchrY_random\t58682461" << endl << endl;
-	cerr << "\t***Only 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;