From 204128fd800af7373b5bea70cd4982e8f3bbcf66 Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Mon, 4 Jan 2010 21:13:34 -0500
Subject: [PATCH] Fixed bug in complementBed vis-a-vis Galaxy.

---
 bin/complementBed                   | Bin 91456 -> 91456 bytes
 obj/complementBed.o                 | Bin 18684 -> 18668 bytes
 src/complementBed/complementBed.cpp |   4 ++--
 3 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/bin/complementBed b/bin/complementBed
index 07dec1d70376bb11889587bac959087c8ee4cb51..c09cd465e028589621860700e1029c75410e0e8b 100755
GIT binary patch
delta 3136
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diff --git a/obj/complementBed.o b/obj/complementBed.o
index 9682f0a77c63043360dde3eb765221e3c976ca2a..2e02c87204bdec7ec8f09308f510f6ae8dd30b58 100644
GIT binary patch
delta 2450
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diff --git a/src/complementBed/complementBed.cpp b/src/complementBed/complementBed.cpp
index e540178c..7c4194a8 100755
--- a/src/complementBed/complementBed.cpp
+++ b/src/complementBed/complementBed.cpp
@@ -80,7 +80,7 @@ void BedComplement::ComplementBed() {
 			}
 			
 			// mask all of the positions spanned by this BED entry.
-			for (int b = bIt->start; b <= bIt->end; b++) {
+			for (int b = bIt->start; b < bIt->end; b++) {
 				chromMasks[b] = 1;
 			}
 		}
@@ -94,7 +94,7 @@ void BedComplement::ComplementBed() {
 					i++;
 				}
 				if (start > 0) {
-					cout << currChrom << "\t" << start -1 << "\t" << i << endl;
+					cout << currChrom << "\t" << start << "\t" << i << endl;
 				}
 				else {
 					cout << currChrom << "\t" << 0 << "\t" << i << endl;
-- 
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