add omitted test dirs for "make test"

test/coverage/one_block.sam

@@ -0,0 +1,3 @@
+@HD	VN:1.0	GO:none	SO:coordinate
+@SQ	SN:chr1	LN:1000
+one_blocks	16	chr1	1	40	30M	*	0	0	GAAGGCCACCGCCGCGGTTATTTTCCTTCA	CCCDDB?=FJIIJIGFJIJHIJJJJJJJJI	MD:Z:50

test/coverage/sam-w-del.sam

@@ -0,0 +1,3 @@
+@HD	VN:1.0	GO:none	SO:coordinate
+@SQ	SN:chr1	LN:1000
+one_bp_del	16	chr1	1	40	10M1D10M	*	0	0	GAAGGCCACCGCCGCGCCGC	CCCDDB?=FJIIJIGIIJIG	MD:Z:50

test/coverage/test-coverage.sh

@@ -0,0 +1,35 @@
+BT=../../bin/bedtools
+
+check()
+{
+	if diff $1 $2; then
+    	echo ok
+	else
+    	echo fail
+	fi
+}
+
+###########################################################
+###########################################################
+#                       BAM files                         #
+###########################################################
+###########################################################
+samtools view -Sb one_block.sam > one_block.bam 2>/dev/null
+samtools view -Sb two_blocks.sam > two_blocks.bam 2>/dev/null
+samtools view -Sb three_blocks.sam > three_blocks.bam 2>/dev/null
+samtools view -Sb sam-w-del.sam > sam-w-del.bam 2>/dev/null
+
+
+
+##################################################################
+#  Test three blocks without -split
+##################################################################
+# echo "    coverage.t1...\c"
+# echo \
+# "chr1	0	50	1" > exp
+# $BT coverage -abam three_blocks.bam -b three_blocks_nomatch.bed > obs
+# check obs exp
+# rm obs exp
+
+
+rm *.bam

test/coverage/three_blocks.sam

@@ -0,0 +1,3 @@
+@HD	VN:1.0	GO:none	SO:coordinate
+@SQ	SN:chr1	LN:1000
+three_blocks	16	chr1	1	40	10M10N10M10N10M	*	0	0	GAAGGCCACCGCCGCGGTTATTTTCCTTCA	CCCDDB?=FJIIJIGFJIJHIJJJJJJJJI	MD:Z:50

test/coverage/three_blocks_match.bed

@@ -0,0 +1 @@
+chr1	0	50	three_blocks_match	0	+	0	0	0	3	10,10,10,	0,20,40,

test/coverage/three_blocks_match_1bp.bed

@@ -0,0 +1 @@
+chr1	10	60	three_blocks_nomatch	0	+	0	0	0	3	11,10,10,	0,20,40,

test/coverage/three_blocks_nomatch.bed

@@ -0,0 +1 @@
+chr1	10	60	three_blocks_nomatch	0	+	0	0	0	3	10,10,10,	0,20,40,

test/coverage/two_blocks.sam

@@ -0,0 +1,3 @@
+@HD	VN:1.0	GO:none	SO:coordinate
+@SQ	SN:chr1	LN:1000
+two_blocks	16	chr1	1	40	15M10N15M	*	0	0	GAAGGCCACCGCCGCGGTTATTTTCCTTCA	CCCDDB?=FJIIJIGFJIJHIJJJJJJJJI	MD:Z:50

test/merge/a.full.bed

@@ -0,0 +1,9 @@
+chr1	10	20	a1	1	+
+chr1	30	40	a2	2	+
+chr1	40	50	a3	3	-
+chr1	45	100	a4	4	+
+chr2	10	20	a1	5	+
+chr2	30	40	a2	6	+
+chr2	42	50	a3	7	+
+chr2	45	100	a4	8	-
+