diff --git a/src/utils/Contexts/ContextIntersect.cpp b/src/utils/Contexts/ContextIntersect.cpp
index 7b4a36d579e28be4b2dc2c7876e1c0301c92585c..1ef4b3d312f4fc6323a1595306828c6fd1eda9f6 100644
--- a/src/utils/Contexts/ContextIntersect.cpp
+++ b/src/utils/Contexts/ContextIntersect.cpp
@@ -231,8 +231,6 @@ bool ContextIntersect::handle_b()
 		int fileId = getNumInputFiles() -1;
 		_dbFileIdxs.push_back(fileId);
 		_fileIdsToDbIdxs[fileId] = _dbFileIdxs.size() -1;
-		int dbFileIdx = getNumInputFiles() -1;
-		_dbFileIdxs.push_back(dbFileIdx);
 		markUsed(_i - _skipFirstArgs);
 		_i++;
 		markUsed(_i - _skipFirstArgs);
diff --git a/src/utils/RecordOutputMgr/RecordOutputMgr.cpp b/src/utils/RecordOutputMgr/RecordOutputMgr.cpp
index d68bd55e231c91d6d3b546fb77b31a4b800aa3be..2d35f07b50f2110000106014c138ef5d211713ad 100644
--- a/src/utils/RecordOutputMgr/RecordOutputMgr.cpp
+++ b/src/utils/RecordOutputMgr/RecordOutputMgr.cpp
@@ -377,7 +377,6 @@ void RecordOutputMgr::addDbFileId(int fileId) {
 	} else {
 		_outBuf.append(_context->getInputFileName(fileId));
 	}
-	_outBuf.append(fileId);
 	tab();
 }
 
diff --git a/test/intersect/multi_intersect/d4.bed~ b/test/intersect/multi_intersect/d4.bed~
deleted file mode 100644
index 91a43d13300eb670f065b5b31097f8c3019951d0..0000000000000000000000000000000000000000
--- a/test/intersect/multi_intersect/d4.bed~
+++ /dev/null
@@ -1,9 +0,0 @@
-chr1	5	25
-chr1	65	75
-chr1	95	100
-chr2	5	25
-chr2	65	75
-chr2	95	100
-chr3	5	25
-chr3	65	75
-chr3	95	100
diff --git a/test/intersect/multi_intersect/d5.bed~ b/test/intersect/multi_intersect/d5.bed~
deleted file mode 100644
index c2b4e526c3278797ef2bfd4fb85625ac452e1128..0000000000000000000000000000000000000000
--- a/test/intersect/multi_intersect/d5.bed~
+++ /dev/null
@@ -1,6 +0,0 @@
-chr1	40	50
-chr1	110	125
-chr2	40	50
-chr2	110	125
-chr3	40	50
-chr3	110	125
diff --git a/test/intersect/multi_intersect/d6.bed~ b/test/intersect/multi_intersect/d6.bed~
deleted file mode 100644
index 46862402f8e7f825026125905fb9653389c976ff..0000000000000000000000000000000000000000
--- a/test/intersect/multi_intersect/d6.bed~
+++ /dev/null
@@ -1,3 +0,0 @@
-chr1	85	115
-chr2	85	115
-chr3	85	115
diff --git a/test/intersect/multi_intersect/d7.bed~ b/test/intersect/multi_intersect/d7.bed~
deleted file mode 100644
index 91a43d13300eb670f065b5b31097f8c3019951d0..0000000000000000000000000000000000000000
--- a/test/intersect/multi_intersect/d7.bed~
+++ /dev/null
@@ -1,9 +0,0 @@
-chr1	5	25
-chr1	65	75
-chr1	95	100
-chr2	5	25
-chr2	65	75
-chr2	95	100
-chr3	5	25
-chr3	65	75
-chr3	95	100
diff --git a/test/intersect/multi_intersect/d8.bed~ b/test/intersect/multi_intersect/d8.bed~
deleted file mode 100644
index c2b4e526c3278797ef2bfd4fb85625ac452e1128..0000000000000000000000000000000000000000
--- a/test/intersect/multi_intersect/d8.bed~
+++ /dev/null
@@ -1,6 +0,0 @@
-chr1	40	50
-chr1	110	125
-chr2	40	50
-chr2	110	125
-chr3	40	50
-chr3	110	125
diff --git a/test/intersect/multi_intersect/d9.bed~ b/test/intersect/multi_intersect/d9.bed~
deleted file mode 100644
index 4fd08cc91d08f14231321bd39decbb7957d27815..0000000000000000000000000000000000000000
--- a/test/intersect/multi_intersect/d9.bed~
+++ /dev/null
@@ -1,4 +0,0 @@
-# DB 9 Header Line. 
-chr1	85	115
-chr2	85	115
-chr3	85	115
diff --git a/test/intersect/multi_intersect/query2.bed~ b/test/intersect/multi_intersect/query2.bed~
deleted file mode 100644
index 3e71c696725466f96e057acd8464b7dcfe9f0843..0000000000000000000000000000000000000000
--- a/test/intersect/multi_intersect/query2.bed~
+++ /dev/null
@@ -1,12 +0,0 @@
-chr1	1	20	q1	100	+
-chr1	40	45	q2	100	+
-chr1	70	90	q3	100	+
-chr1	105	120	q4	100	+
-chr2	1	20	q5	100	+
-chr2	40	45	q6	100	+
-chr2	70	90	q7	100	+
-chr2	105	120	q8	100	+
-chr10	1	20	q9	100	+
-chr10	40	45	q10	100	+
-chr10	70	90	q11	100	+
-chr10	105	120	q12	100	+
diff --git a/test/intersect/multi_intersect/query3.bed~ b/test/intersect/multi_intersect/query3.bed~
deleted file mode 100644
index 91b5adfdbb3c59a62f3e26073c35554bb76d444d..0000000000000000000000000000000000000000
--- a/test/intersect/multi_intersect/query3.bed~
+++ /dev/null
@@ -1,13 +0,0 @@
-# Query 2 Header Line.
-chr1	1	20	q1	100	+
-chr1	40	45	q2	100	+
-chr1	70	90	q3	100	+
-chr1	105	120	q4	100	+
-chr2	1	20	q5	100	+
-chr2	40	45	q6	100	+
-chr2	70	90	q7	100	+
-chr2	105	120	q8	100	+
-chr10	1	20	q9	100	+
-chr10	40	45	q10	100	+
-chr10	70	90	q11	100	+
-chr10	105	120	q12	100	+
diff --git a/test/intersect/multi_intersect/test-multi_intersect.sh~ b/test/intersect/multi_intersect/test-multi_intersect.sh~
deleted file mode 100644
index a0d44e4bb5132a826c601447a57c1fa7d159a9a5..0000000000000000000000000000000000000000
--- a/test/intersect/multi_intersect/test-multi_intersect.sh~
+++ /dev/null
@@ -1,404 +0,0 @@
-echo -e \
-"\n###########################################################
-#  
-#  MULTIPLE DATABASE INTERSECTION
-#
-###########################################################\n"
-
-
-BT=${BT-../../../bin/bedtools}
-
-check()
-{
-	if diff $1 $2; then
-    	echo ok
-	else
-    	echo fail
-	fi
-}
-
-###########################################################
-#  Test the intersection of a query with 3 dbs against 
-#  the merged and sorted result of 3 
-#  seperate intersections of the query with each db.
-#
-#  First make sure the 3 seperate intersections are correct.
-#
-############################################################
-echo "    intersect.t01...\c"
-echo \
-"chr1	5	20
-chr1	70	75
-chr2	5	20
-chr2	70	75
-chr3	5	20
-chr3	70	75" > exp1 
-$BT intersect -a query.bed -b d1.bed > obs
-check obs exp1
-rm obs
-
-echo "    intersect.t02...\c"
-echo \
-"chr1	40	45
-chr1	110	120
-chr2	40	45
-chr2	110	120
-chr3	40	45
-chr3	110	120" > exp2
-$BT intersect -a query.bed -b d2.bed > obs
-check obs exp2
-rm obs
-
-echo "    intersect.t03...\c"
-echo \
-"chr1	85	90
-chr1	105	115
-chr2	85	90
-chr2	105	115
-chr3	85	90
-chr3	105	115" > exp3
-$BT intersect -a query.bed -b d3.bed > obs
-check obs exp3
-rm obs
-
-###########################################################
-#  Now test that the R-tree (unsorted input) with sorted
-#  output will give the correct result
-###########################################################
-echo "    intersect.t04...\c"
-cat exp1 exp2 exp3 | sort -k1,1 -k2,2n > exp
-$BT intersect -a query.bed -b d1.bed d2.bed d3.bed -sortout > obs
-check exp obs
-rm obs exp1 exp2 exp3
-
-
-###########################################################
-#  And then test that sorted input with sorted
-#  output will give the correct result
-###########################################################
-echo "    intersect.t05...\c"
-$BT intersect -a query.bed -b d1.bed d2.bed d3.bed -sorted -sortout > obs
-check exp obs
-rm obs exp
-
-
-###########################################################
-# 
-#  Now repeat the above with chroms in a non-standard order
-#
-###########################################################
-
-echo "    intersect.t06...\c"
-echo \
-"chr1	5	20
-chr1	70	75
-chr2	5	20
-chr2	70	75
-chr10	5	20
-chr10	70	75" > exp1 
-$BT intersect -a query2.bed -b d4.bed > obs
-check obs exp1
-rm obs
-
-echo "    intersect.t07...\c"
-echo \
-"chr1	40	45
-chr1	110	120
-chr2	40	45
-chr2	110	120
-chr10	40	45
-chr10	110	120" > exp2
-$BT intersect -a query2.bed -b d5.bed > obs
-check obs exp2
-rm obs
-
-echo "    intersect.t08...\c"
-echo \
-"chr1	85	90
-chr1	105	115
-chr2	85	90
-chr2	105	115
-chr10	85	90
-chr10	105	115" > exp3
-$BT intersect -a query2.bed -b d6.bed > obs
-check obs exp3
-rm obs
-
-###########################################################
-#  Now test that the R-tree (unsorted input) with sorted
-#  output will give the correct result
-###########################################################
-echo "    intersect.t09...\c"
-cat exp1 exp2 exp3 | sort -k1,1V -k2,2n > exp
-$BT intersect -a query2.bed -b d4.bed d5.bed d6.bed -g g.bed -sortout > obs
-check exp obs
-rm obs exp1 exp2 exp3
-
-
-###########################################################
-#  And then test that sorted input with sorted
-#  output will give the correct result
-###########################################################
-echo "    intersect.t10...\c"
-$BT intersect -a query2.bed -b d4.bed d5.bed d6.bed -sorted -g g.bed -sortout > obs
-check exp obs
-rm obs exp
-
-
-
-###########################################################
-# 
-# TEST VARIOUS CMD LINE OUTPUT OPTIONS
-#
-###########################################################
-
-
-###########################################################
-#  Test -c option
-###########################################################
-echo "    intersect.t11...\c"
-echo \
-"chr1	1	20	1
-chr1	40	45	1
-chr1	70	90	2
-chr1	105	120	2
-chr2	1	20	1
-chr2	40	45	1
-chr2	70	90	2
-chr2	105	120	2
-chr3	1	20	1
-chr3	40	45	1
-chr3	70	90	2
-chr3	105	120	2" > exp
-$BT intersect -a query.bed -b d1.bed d2.bed d3.bed -c -sorted -sortout > obs
-check exp obs
-rm exp obs
-
-
-###########################################################
-#  Test -f option
-###########################################################
-echo "    intersect.t12...\c"
-echo \
-"chr1	5	20
-chr1	40	45
-chr1	110	120
-chr1	105	115
-chr2	5	20
-chr2	40	45
-chr2	110	120
-chr2	105	115
-chr3	5	20
-chr3	40	45
-chr3	110	120
-chr3	105	115" > exp
-$BT intersect -a query.bed -b d1.bed d2.bed d3.bed -f .6 > obs
-check exp obs
-
-
-###########################################################
-#  Test -s option
-###########################################################
-echo "    intersect.t13...\c"
-echo \
-"chr1	5	20	q1	100	+
-chr1	85	90	q3	100	+
-chr1	110	120	q4	100	+
-chr1	105	115	q4	100	+
-chr3	5	20	q9	100	+
-chr3	85	90	q11	100	+
-chr3	110	120	q12	100	+
-chr3	105	115	q12	100	+" > exp
-$BT intersect -a query3.bed -b d7.bed d8.bed d9.bed -s > obs
-check exp obs
-rm exp obs
-
-
-###########################################################
-#  Test -s option
-###########################################################
-echo "    intersect.t13...\c"
-echo \
-"chr1	40	45	q2	100	+
-chr1	70	75	q3	100	+
-chr2	5	20	q5	100	+
-chr2	40	45	q6	100	+
-chr2	85	90	q7	100	+
-chr2	105	115	q8	100	+
-chr3	40	45	q10	100	+
-chr3	70	75	q11	100	+" > exp
-$BT intersect -a query3.bed -b d7.bed d8.bed d9.bed -S > obs
-check exp obs
-rm exp obs
-
-
-###########################################################
-#  Test -wo option
-###########################################################
-echo "    intersect.t14...\c"
-echo \
-"chr1	1	20	1	chr1	5	25	15
-chr1	40	45	2	chr1	40	50	5
-chr1	70	90	1	chr1	65	75	5
-chr1	70	90	3	chr1	85	115	5
-chr1	105	120	2	chr1	110	125	10
-chr1	105	120	3	chr1	85	115	10
-chr2	1	20	1	chr2	5	25	15
-chr2	40	45	2	chr2	40	50	5
-chr2	70	90	1	chr2	65	75	5
-chr2	70	90	3	chr2	85	115	5
-chr2	105	120	2	chr2	110	125	10
-chr2	105	120	3	chr2	85	115	10
-chr3	1	20	1	chr3	5	25	15
-chr3	40	45	2	chr3	40	50	5
-chr3	70	90	1	chr3	65	75	5
-chr3	70	90	3	chr3	85	115	5
-chr3	105	120	2	chr3	110	125	10
-chr3	105	120	3	chr3	85	115	10" > exp
-$BT intersect -a query.bed -b d1.bed d2.bed d3.bed -wo > obs
-check exp obs
-rm exp obs
-
-
-
-###########################################################
-#  Test -wa -wb -header option
-###########################################################
-echo "    intersect.t15...\c"
-echo \
-"# Query 3 Header Line.
-chr1	1	20	q1	100	+	1	chr1	5	25	d7_1	100	+
-chr1	40	45	q2	100	+	2	chr1	40	50	d8_1	100	-
-chr1	70	90	q3	100	+	1	chr1	65	75	d7_2	100	-
-chr1	70	90	q3	100	+	3	chr1	85	115	d9_1	100	+
-chr1	105	120	q4	100	+	2	chr1	110	125	d8_2	100	+
-chr1	105	120	q4	100	+	3	chr1	85	115	d9_1	100	+
-chr2	1	20	q5	100	+	1	chr2	5	25	d7_4	100	-
-chr2	40	45	q6	100	+	2	chr2	40	50	d8_3	100	-
-chr2	70	90	q7	100	+	1	chr2	65	75	d7_5	100	.
-chr2	70	90	q7	100	+	3	chr2	85	115	d9_1	100	-
-chr2	105	120	q8	100	+	2	chr2	110	125	d8_4	100	.
-chr2	105	120	q8	100	+	3	chr2	85	115	d9_1	100	-
-chr3	1	20	q9	100	+	1	chr3	5	25	d7_7	100	+
-chr3	40	45	q10	100	+	2	chr3	40	50	d8_5	100	-
-chr3	70	90	q11	100	+	1	chr3	65	75	d7_8	100	-
-chr3	70	90	q11	100	+	3	chr3	85	115	d9_1	100	+
-chr3	105	120	q12	100	+	2	chr3	110	125	d8_6	100	+
-chr3	105	120	q12	100	+	3	chr3	85	115	d9_1	100	+" > exp
-$BT intersect -a query3.bed -b d7.bed d8.bed d9.bed -wa -wb -header > obs
-check exp obs
-rm exp obs
-
-
-
-###########################################################
-#  Test the -filenames option, before db listing
-###########################################################
-echo "    intersect.t16...\c"
-echo \
-"chr1	1	20	q1	100	+	d7.bed	chr1	5	25	d7_1	100	+
-chr1	40	45	q2	100	+	d8.bed	chr1	40	50	d8_1	100	-
-chr1	70	90	q3	100	+	d7.bed	chr1	65	75	d7_2	100	-
-chr1	70	90	q3	100	+	d9.bed	chr1	85	115	d9_1	100	+
-chr1	105	120	q4	100	+	d8.bed	chr1	110	125	d8_2	100	+
-chr1	105	120	q4	100	+	d9.bed	chr1	85	115	d9_1	100	+
-chr2	1	20	q5	100	+	d7.bed	chr2	5	25	d7_4	100	-
-chr2	40	45	q6	100	+	d8.bed	chr2	40	50	d8_3	100	-
-chr2	70	90	q7	100	+	d7.bed	chr2	65	75	d7_5	100	.
-chr2	70	90	q7	100	+	d9.bed	chr2	85	115	d9_1	100	-
-chr2	105	120	q8	100	+	d8.bed	chr2	110	125	d8_4	100	.
-chr2	105	120	q8	100	+	d9.bed	chr2	85	115	d9_1	100	-
-chr3	1	20	q9	100	+	d7.bed	chr3	5	25	d7_7	100	+
-chr3	40	45	q10	100	+	d8.bed	chr3	40	50	d8_5	100	-
-chr3	70	90	q11	100	+	d7.bed	chr3	65	75	d7_8	100	-
-chr3	70	90	q11	100	+	d9.bed	chr3	85	115	d9_1	100	+
-chr3	105	120	q12	100	+	d8.bed	chr3	110	125	d8_6	100	+
-chr3	105	120	q12	100	+	d9.bed	chr3	85	115	d9_1	100	+" > exp
-$BT intersect -a query3.bed -filenames -b d7.bed d8.bed d9.bed -wa -wb > obs
-check exp obs
-rm exp obs
-
-###########################################################
-#  Test the -filenames option, after db listing
-###########################################################
-echo "    intersect.t17...\c"
-echo \
-"chr1	1	20	q1	100	+	d7.bed	chr1	5	25	d7_1	100	+
-chr1	40	45	q2	100	+	d8.bed	chr1	40	50	d8_1	100	-
-chr1	70	90	q3	100	+	d7.bed	chr1	65	75	d7_2	100	-
-chr1	70	90	q3	100	+	d9.bed	chr1	85	115	d9_1	100	+
-chr1	105	120	q4	100	+	d8.bed	chr1	110	125	d8_2	100	+
-chr1	105	120	q4	100	+	d9.bed	chr1	85	115	d9_1	100	+
-chr2	1	20	q5	100	+	d7.bed	chr2	5	25	d7_4	100	-
-chr2	40	45	q6	100	+	d8.bed	chr2	40	50	d8_3	100	-
-chr2	70	90	q7	100	+	d7.bed	chr2	65	75	d7_5	100	.
-chr2	70	90	q7	100	+	d9.bed	chr2	85	115	d9_1	100	-
-chr2	105	120	q8	100	+	d8.bed	chr2	110	125	d8_4	100	.
-chr2	105	120	q8	100	+	d9.bed	chr2	85	115	d9_1	100	-
-chr3	1	20	q9	100	+	d7.bed	chr3	5	25	d7_7	100	+
-chr3	40	45	q10	100	+	d8.bed	chr3	40	50	d8_5	100	-
-chr3	70	90	q11	100	+	d7.bed	chr3	65	75	d7_8	100	-
-chr3	70	90	q11	100	+	d9.bed	chr3	85	115	d9_1	100	+
-chr3	105	120	q12	100	+	d8.bed	chr3	110	125	d8_6	100	+
-chr3	105	120	q12	100	+	d9.bed	chr3	85	115	d9_1	100	+" > exp
-$BT intersect -a query3.bed -b d7.bed d8.bed d9.bed -filenames -wa -wb > obs
-check exp obs
-rm exp obs
-
-
-###########################################################
-#  Test the -names option, before db listing
-###########################################################
-echo "    intersect.t18...\c"
-echo \
-"chr1	1	20	q1	100	+	blue	chr1	5	25	d7_1	100	+
-chr1	40	45	q2	100	+	red	chr1	40	50	d8_1	100	-
-chr1	70	90	q3	100	+	blue	chr1	65	75	d7_2	100	-
-chr1	70	90	q3	100	+	green	chr1	85	115	d9_1	100	+
-chr1	105	120	q4	100	+	red	chr1	110	125	d8_2	100	+
-chr1	105	120	q4	100	+	green	chr1	85	115	d9_1	100	+
-chr2	1	20	q5	100	+	blue	chr2	5	25	d7_4	100	-
-chr2	40	45	q6	100	+	red	chr2	40	50	d8_3	100	-
-chr2	70	90	q7	100	+	blue	chr2	65	75	d7_5	100	.
-chr2	70	90	q7	100	+	green	chr2	85	115	d9_1	100	-
-chr2	105	120	q8	100	+	red	chr2	110	125	d8_4	100	.
-chr2	105	120	q8	100	+	green	chr2	85	115	d9_1	100	-
-chr3	1	20	q9	100	+	blue	chr3	5	25	d7_7	100	+
-chr3	40	45	q10	100	+	red	chr3	40	50	d8_5	100	-
-chr3	70	90	q11	100	+	blue	chr3	65	75	d7_8	100	-
-chr3	70	90	q11	100	+	green	chr3	85	115	d9_1	100	+
-chr3	105	120	q12	100	+	red	chr3	110	125	d8_6	100	+
-chr3	105	120	q12	100	+	green	chr3	85	115	d9_1	100	+" > exp
-$BT intersect -a query3.bed -names blue red green -b d7.bed d8.bed d9.bed -wa -wb > obs
-check exp obs
-rm exp obs
-
-###########################################################
-#  Test the -names option, after db listing
-###########################################################
-echo "    intersect.t18...\c"
-echo \
-"chr1	1	20	q1	100	+	blue	chr1	5	25	d7_1	100	+
-chr1	40	45	q2	100	+	red	chr1	40	50	d8_1	100	-
-chr1	70	90	q3	100	+	blue	chr1	65	75	d7_2	100	-
-chr1	70	90	q3	100	+	green	chr1	85	115	d9_1	100	+
-chr1	105	120	q4	100	+	red	chr1	110	125	d8_2	100	+
-chr1	105	120	q4	100	+	green	chr1	85	115	d9_1	100	+
-chr2	1	20	q5	100	+	blue	chr2	5	25	d7_4	100	-
-chr2	40	45	q6	100	+	red	chr2	40	50	d8_3	100	-
-chr2	70	90	q7	100	+	blue	chr2	65	75	d7_5	100	.
-chr2	70	90	q7	100	+	green	chr2	85	115	d9_1	100	-
-chr2	105	120	q8	100	+	red	chr2	110	125	d8_4	100	.
-chr2	105	120	q8	100	+	green	chr2	85	115	d9_1	100	-
-chr3	1	20	q9	100	+	blue	chr3	5	25	d7_7	100	+
-chr3	40	45	q10	100	+	red	chr3	40	50	d8_5	100	-
-chr3	70	90	q11	100	+	blue	chr3	65	75	d7_8	100	-
-chr3	70	90	q11	100	+	green	chr3	85	115	d9_1	100	+
-chr3	105	120	q12	100	+	red	chr3	110	125	d8_6	100	+
-chr3	105	120	q12	100	+	green	chr3	85	115	d9_1	100	+" > exp
-$BT intersect -a query3.bed -b d7.bed d8.bed d9.bed -names blue red green -wa -wb > obs
-check exp obs
-rm exp obs
-
-
-