diff --git a/src/intersectBed/intersectBed.cpp b/src/intersectBed/intersectBed.cpp
index 1d410ae16f23994ef30ee00ac68b24fa4f232bcb..229300bc5d1188a13d20934efd7506e09a6b4892 100644
--- a/src/intersectBed/intersectBed.cpp
+++ b/src/intersectBed/intersectBed.cpp
@@ -328,7 +328,7 @@ void BedIntersect::IntersectBam(string bamFile) {
BED bed;
MakeBedFromBam(bam, chrom, bed_blocks, bed);
bool overlapsFound = false;
- if ((_bamOutput == true) && (_obeySplits == false))
+ if ((_bamOutput == true) && (_obeySplits == false))
{
overlapsFound = _bedB->anyHits(bed.chrom, bed.start, bed.end,
bed.strand, _sameStrand, _diffStrand,
diff --git a/src/mapBed/mapBed.cpp b/src/mapBed/mapBed.cpp
index d8051103a2ebe0b7d41887649f2c84e702e50ad2..6c5b2be539b62f9ee41da6f122a33ad264831855 100644
--- a/src/mapBed/mapBed.cpp
+++ b/src/mapBed/mapBed.cpp
@@ -19,7 +19,8 @@ double GetUserColumn(const string s);
BedMap::BedMap(string bedAFile, string bedBFile, int column, string operation,
float overlapFraction, bool sameStrand,
bool diffStrand, bool reciprocal,
- string nullValue, bool printHeader)
+ bool choseNullValue, string nullValue,
+ bool printHeader)
{
_bedAFile = bedAFile;
@@ -33,6 +34,8 @@ BedMap::BedMap(string bedAFile, string bedBFile, int column, string operation,
_nullValue = nullValue;
_printHeader = printHeader;
+ if (!choseNullValue && operation == "count")
+ _nullValue = "0";
Map();
}
@@ -84,7 +87,7 @@ string BedMap::MapHits(const BED &a, const vector<BED> &hits) {
output << vo.GetMode();
else if (_operation == "antimode")
output << vo.GetAntiMode();
- else if (_operation == "count")
+ else if (_operation == "count")
output << setprecision (PRECISION) << vo.GetCount();
else if (_operation == "count_distinct")
output << setprecision (PRECISION) << vo.GetCountDistinct();
diff --git a/src/mapBed/mapBed.h b/src/mapBed/mapBed.h
index 91dfa10794f5db9b7cef6002da01f0f289935b49..f8cc5de12678291263a07f0d20a092b5bfcfdaa2 100644
--- a/src/mapBed/mapBed.h
+++ b/src/mapBed/mapBed.h
@@ -41,7 +41,8 @@ public:
BedMap(string bedAFile, string bedBFile, int column, string operation,
float overlapFraction, bool sameStrand,
bool diffStrand, bool reciprocal,
- string nullValue, bool printHeader);
+ bool choseNullValue, string nullValue,
+ bool printHeader);
// destructor
~BedMap(void);
diff --git a/src/mapBed/mapMain.cpp b/src/mapBed/mapMain.cpp
index 1ecf6869c105b3f62b395aff40cd694fb6e705ee..8f1559d54c682a182b78a8b9e862550ab62ad6b0 100644
--- a/src/mapBed/mapMain.cpp
+++ b/src/mapBed/mapMain.cpp
@@ -48,6 +48,7 @@ int map_main(int argc, char* argv[]) {
bool sameStrand = false;
bool diffStrand = false;
bool printHeader = false;
+ bool choseNullValue = false;
// check to see if we should print out some help
if(argc <= 1) showHelp = true;
@@ -114,6 +115,7 @@ int map_main(int argc, char* argv[]) {
}
else if (PARAMETER_CHECK("-null", 5, parameterLength)) {
nullValue = argv[i + 1];
+ choseNullValue = true;
i++;
}
else if(PARAMETER_CHECK("-header", 7, parameterLength)) {
@@ -146,7 +148,8 @@ int map_main(int argc, char* argv[]) {
BedMap *bm = new BedMap(bedAFile, bedBFile, column, operation,
overlapFraction, sameStrand,
diffStrand, reciprocalFraction,
- nullValue, printHeader);
+ choseNullValue, nullValue,
+ printHeader);
delete bm;
return 0;
}
diff --git a/test/bamtobed/one_block.sam b/test/bamtobed/one_block.sam
new file mode 100644
index 0000000000000000000000000000000000000000..83041cf531ddf8ca5c02e3175509fa983953d9f0
--- /dev/null
+++ b/test/bamtobed/one_block.sam
@@ -0,0 +1,3 @@
+@HD VN:1.0 GO:none SO:coordinate
+@SQ SN:chr1 LN:249250621
+one_blocks 16 chr1 1 40 30M * 0 0 GAAGGCCACCGCCGCGGTTATTTTCCTTCA CCCDDB?=FJIIJIGFJIJHIJJJJJJJJI MD:Z:50
diff --git a/test/bamtobed/test-bamtobed.sh b/test/bamtobed/test-bamtobed.sh
new file mode 100644
index 0000000000000000000000000000000000000000..0d028e74e038fb0026bd1f521812adde6f4deff3
--- /dev/null
+++ b/test/bamtobed/test-bamtobed.sh
@@ -0,0 +1,113 @@
+BT=../../bin/bedtools
+
+check()
+{
+ if diff $1 $2; then
+ echo ok
+ else
+ echo fail
+ fi
+}
+
+###########################################################
+###########################################################
+# BAM files #
+###########################################################
+###########################################################
+samtools view -Sb one_block.sam > one_block.bam 2>/dev/null
+samtools view -Sb two_blocks.sam > two_blocks.bam 2>/dev/null
+samtools view -Sb three_blocks.sam > three_blocks.bam 2>/dev/null
+samtools view -Sb sam-w-del.sam > sam-w-del.bam 2>/dev/null
+
+
+##################################################################
+# Test one block without -split
+##################################################################
+echo " bamtobed.t1...\c"
+echo \
+"chr1 0 30 one_blocks 40 -" > exp
+$BT bamtobed -i one_block.bam > obs
+check obs exp
+rm obs exp
+
+
+##################################################################
+# Test one block with -split
+##################################################################
+echo " bamtobed.t2...\c"
+echo \
+"chr1 0 30 one_blocks 40 -" > exp
+$BT bamtobed -i one_block.bam -split > obs
+check obs exp
+rm obs exp
+
+
+##################################################################
+# Test two blocks without -split
+##################################################################
+echo " bamtobed.t3...\c"
+echo \
+"chr1 0 40 two_blocks 40 -" > exp
+$BT bamtobed -i two_blocks.bam > obs
+check obs exp
+rm obs exp
+
+
+##################################################################
+# Test two blocks with -split
+##################################################################
+echo " bamtobed.t4...\c"
+echo \
+"chr1 0 15 two_blocks 40 -
+chr1 25 40 two_blocks 40 -" > exp
+$BT bamtobed -i two_blocks.bam -split > obs
+check obs exp
+rm obs exp
+
+
+##################################################################
+# Test three blocks without -split
+##################################################################
+echo " bamtobed.t5...\c"
+echo \
+"chr1 0 50 three_blocks 40 -" > exp
+$BT bamtobed -i three_blocks.bam > obs
+check obs exp
+rm obs exp
+
+
+##################################################################
+# Test three blocks with -split
+##################################################################
+echo " bamtobed.t6...\c"
+echo \
+"chr1 0 10 three_blocks 40 -
+chr1 20 30 three_blocks 40 -
+chr1 40 50 three_blocks 40 -" > exp
+$BT bamtobed -i three_blocks.bam -split > obs
+check obs exp
+rm obs exp
+
+
+##################################################################
+# Test three blocks with -bed12
+##################################################################
+echo " bamtobed.t7...\c"
+echo \
+"chr1 0 50 three_blocks 40 - 0 50 255,0,0 3 10,10,10 0,20,40" > exp
+$BT bamtobed -i three_blocks.bam -bed12 > obs
+check obs exp
+rm obs exp
+
+
+##################################################################
+# Ensure that both ways of getting blocks from a spliced alignment
+# are indenticsl
+##################################################################
+echo " bamtobed.t8...\c"
+$BT bamtobed -i three_blocks.bam -split > split
+$BT bamtobed -i three_blocks.bam -bed12 | $BT bed12tobed6 > bed12
+check split bed12
+rm split bed12
+
+rm *.bam
diff --git a/test/bamtobed/three_blocks.sam b/test/bamtobed/three_blocks.sam
new file mode 100644
index 0000000000000000000000000000000000000000..6e3bc601a7135401ddcadcff667be01bbd30a62a
--- /dev/null
+++ b/test/bamtobed/three_blocks.sam
@@ -0,0 +1,3 @@
+@HD VN:1.0 GO:none SO:coordinate
+@SQ SN:chr1 LN:249250621
+three_blocks 16 chr1 1 40 10M10N10M10N10M * 0 0 GAAGGCCACCGCCGCGGTTATTTTCCTTCA CCCDDB?=FJIIJIGFJIJHIJJJJJJJJI MD:Z:50
diff --git a/test/bamtobed/two_blocks.sam b/test/bamtobed/two_blocks.sam
new file mode 100644
index 0000000000000000000000000000000000000000..6f19dcf93903dc6eed1548121bdb11bc0e9625cc
--- /dev/null
+++ b/test/bamtobed/two_blocks.sam
@@ -0,0 +1,3 @@
+@HD VN:1.0 GO:none SO:coordinate
+@SQ SN:chr1 LN:249250621
+two_blocks 16 chr1 1 40 15M10N15M * 0 0 GAAGGCCACCGCCGCGGTTATTTTCCTTCA CCCDDB?=FJIIJIGFJIJHIJJJJJJJJI MD:Z:50
\ No newline at end of file
diff --git a/test/bed12tobed6/bed6.bed b/test/bed12tobed6/bed6.bed
new file mode 100644
index 0000000000000000000000000000000000000000..e3a0a98570b76bcad9423b2b24e797e1e9fe2ccb
--- /dev/null
+++ b/test/bed12tobed6/bed6.bed
@@ -0,0 +1 @@
+chr1 0 50 bed6 1 +
\ No newline at end of file
diff --git a/test/bed12tobed6/one_blocks.bed b/test/bed12tobed6/one_blocks.bed
new file mode 100644
index 0000000000000000000000000000000000000000..a26047796cb9674eaaef187459185bb622db0e42
--- /dev/null
+++ b/test/bed12tobed6/one_blocks.bed
@@ -0,0 +1 @@
+chr1 0 50 one_blocks_match 0 + 0 0 0 1 50, 0,
diff --git a/test/bed12tobed6/test-bed12tobed6.sh b/test/bed12tobed6/test-bed12tobed6.sh
new file mode 100644
index 0000000000000000000000000000000000000000..1cc53e86472c5f8905a0ab9d533ec0ffb0727a9c
--- /dev/null
+++ b/test/bed12tobed6/test-bed12tobed6.sh
@@ -0,0 +1,71 @@
+BT=../../bin/bedtools
+
+check()
+{
+ if diff $1 $2; then
+ echo ok
+ else
+ echo fail
+ fi
+}
+
+
+##################################################################
+# Test one block
+##################################################################
+echo " bed12tobed6.t1...\c"
+echo \
+"chr1 0 50 one_blocks_match 0 +" > exp
+$BT bed12tobed6 -i one_blocks.bed > obs
+check obs exp
+rm obs exp
+
+
+##################################################################
+# Test two blocks
+##################################################################
+echo " bed12tobed6.t2...\c"
+echo \
+"chr1 0 10 two_blocks_match 0 +
+chr1 40 50 two_blocks_match 0 +" > exp
+$BT bed12tobed6 -i two_blocks.bed > obs
+check obs exp
+rm obs exp
+
+##################################################################
+# Test three blocks
+##################################################################
+echo " bed12tobed6.t3...\c"
+echo \
+"chr1 0 10 three_blocks_match 0 +
+chr1 20 30 three_blocks_match 0 +
+chr1 40 50 three_blocks_match 0 +" > exp
+$BT bed12tobed6 -i three_blocks.bed > obs
+check obs exp
+rm obs exp
+
+
+##################################################################
+# Test three blocks and add block numbers
+##################################################################
+echo " bed12tobed6.t4...\c"
+echo \
+"chr1 0 10 three_blocks_match 1 +
+chr1 20 30 three_blocks_match 2 +
+chr1 40 50 three_blocks_match 3 +" > exp
+$BT bed12tobed6 -i three_blocks.bed -n > obs
+check obs exp
+rm obs exp
+
+
+##################################################################
+# Test three blocks and add block numbers. Test reverse strand
+##################################################################
+echo " bed12tobed6.t5...\c"
+echo \
+"chr1 0 10 three_blocks_match 3 -
+chr1 20 30 three_blocks_match 2 -
+chr1 40 50 three_blocks_match 1 -" > exp
+sed -e 's/\+/\-/' three_blocks.bed | $BT bed12tobed6 -n > obs
+check obs exp
+rm obs exp
\ No newline at end of file
diff --git a/test/bed12tobed6/three_blocks.bed b/test/bed12tobed6/three_blocks.bed
new file mode 100644
index 0000000000000000000000000000000000000000..33123c2f69f08c6dce7cf093cb07be44bb5f9113
--- /dev/null
+++ b/test/bed12tobed6/three_blocks.bed
@@ -0,0 +1 @@
+chr1 0 50 three_blocks_match 0 + 0 0 0 3 10,10,10, 0,20,40,
diff --git a/test/bed12tobed6/two_blocks.bed b/test/bed12tobed6/two_blocks.bed
new file mode 100644
index 0000000000000000000000000000000000000000..5fcfa6d5e216e9ebacec003d5b4cf92fd14dd8d6
--- /dev/null
+++ b/test/bed12tobed6/two_blocks.bed
@@ -0,0 +1 @@
+chr1 0 50 two_blocks_match 0 + 0 0 0 2 10,10, 0,40,
diff --git a/test/genomecov/one_block.sam b/test/genomecov/one_block.sam
new file mode 100644
index 0000000000000000000000000000000000000000..48408220f9be16e51cf76271f62eeb26b3d03988
--- /dev/null
+++ b/test/genomecov/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
\ No newline at end of file
diff --git a/test/genomecov/sam-w-del.sam b/test/genomecov/sam-w-del.sam
new file mode 100644
index 0000000000000000000000000000000000000000..887b745d8a6bc79f1d4c7fbba14cb2985f1a57f0
--- /dev/null
+++ b/test/genomecov/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
diff --git a/test/genomecov/test-genomecov.sh b/test/genomecov/test-genomecov.sh
new file mode 100644
index 0000000000000000000000000000000000000000..b7102d5d0f95918721a94e62f9336de665671ede
--- /dev/null
+++ b/test/genomecov/test-genomecov.sh
@@ -0,0 +1,147 @@
+BT=../../bin/bedtools
+
+check()
+{
+ if diff $1 $2; then
+ echo ok
+ else
+ echo fail
+ fi
+}
+
+###########################################################
+###########################################################
+# BAM files #
+###########################################################
+###########################################################
+samtools view -Sb one_block.sam > one_block.bam 2>/dev/null
+samtools view -Sb two_blocks.sam > two_blocks.bam 2>/dev/null
+samtools view -Sb three_blocks.sam > three_blocks.bam 2>/dev/null
+samtools view -Sb sam-w-del.sam > sam-w-del.bam 2>/dev/null
+
+
+
+##################################################################
+# Test three blocks without -split
+##################################################################
+echo " genomecov.t1...\c"
+echo \
+"chr1 0 50 1" > exp
+$BT genomecov -ibam three_blocks.bam -bg > obs
+check obs exp
+rm obs exp
+
+
+##################################################################
+# Test three blocks with -split
+##################################################################
+echo " genomecov.t2...\c"
+echo \
+"chr1 0 10 1
+chr1 20 30 1
+chr1 40 50 1" > exp
+$BT genomecov -ibam three_blocks.bam -bg -split > obs
+check obs exp
+rm obs exp
+
+
+##################################################################
+# Test three blocks with -split and -bga
+##################################################################
+echo " genomecov.t3...\c"
+echo \
+"chr1 0 10 1
+chr1 10 20 0
+chr1 20 30 1
+chr1 30 40 0
+chr1 40 50 1
+chr1 50 1000 0" > exp
+$BT genomecov -ibam three_blocks.bam -bga -split > obs
+check obs exp
+rm obs exp
+
+
+##################################################################
+# Test blocked BAM from multiple files w/ -bga and w/o -split
+##################################################################
+echo " genomecov.t4...\c"
+echo \
+"chr1 0 30 3
+chr1 30 40 2
+chr1 40 50 1
+chr1 50 1000 0" > exp
+samtools merge -f /dev/stdout *block*.bam | $BT genomecov -ibam - -bga > obs
+check obs exp
+rm obs exp
+
+
+##################################################################
+# Test blocked BAM from multiple files w/ -bga and w -split
+##################################################################
+echo " genomecov.t5...\c"
+echo \
+"chr1 0 10 3
+chr1 10 15 2
+chr1 15 20 1
+chr1 20 25 2
+chr1 25 30 3
+chr1 30 50 1
+chr1 50 1000 0" > exp
+samtools merge -f /dev/stdout *block*.bam | $BT genomecov -ibam - -bga -split > obs
+check obs exp
+rm obs exp
+
+
+##################################################################
+# Test three blocks with -split and -dz
+##################################################################
+echo " genomecov.t6...\c"
+echo \
+"chr1 0 1
+chr1 1 1
+chr1 2 1
+chr1 3 1
+chr1 4 1
+chr1 5 1
+chr1 6 1
+chr1 7 1
+chr1 8 1
+chr1 9 1
+chr1 20 1
+chr1 21 1
+chr1 22 1
+chr1 23 1
+chr1 24 1
+chr1 25 1
+chr1 26 1
+chr1 27 1
+chr1 28 1
+chr1 29 1
+chr1 40 1
+chr1 41 1
+chr1 42 1
+chr1 43 1
+chr1 44 1
+chr1 45 1
+chr1 46 1
+chr1 47 1
+chr1 48 1
+chr1 49 1" > exp
+$BT genomecov -ibam three_blocks.bam -dz -split > obs
+check obs exp
+rm obs exp
+
+
+##################################################################
+# Test SAM with 1bp D operator
+##################################################################
+echo " genomecov.t7...\c"
+echo \
+"chr1 0 10 1
+chr1 11 21 1" > exp
+$BT genomecov -ibam sam-w-del.bam -bg > obs
+check obs exp
+rm obs exp
+
+
+rm *.bam
\ No newline at end of file
diff --git a/test/genomecov/three_blocks.sam b/test/genomecov/three_blocks.sam
new file mode 100644
index 0000000000000000000000000000000000000000..9bf1a62796d23b7a8cb92a016c32fcef748d45cc
--- /dev/null
+++ b/test/genomecov/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
diff --git a/test/genomecov/three_blocks_match.bed b/test/genomecov/three_blocks_match.bed
new file mode 100644
index 0000000000000000000000000000000000000000..33123c2f69f08c6dce7cf093cb07be44bb5f9113
--- /dev/null
+++ b/test/genomecov/three_blocks_match.bed
@@ -0,0 +1 @@
+chr1 0 50 three_blocks_match 0 + 0 0 0 3 10,10,10, 0,20,40,
diff --git a/test/genomecov/three_blocks_match_1bp.bed b/test/genomecov/three_blocks_match_1bp.bed
new file mode 100644
index 0000000000000000000000000000000000000000..de8b10d2b4a259eebdf71d7995d930ee23c69af6
--- /dev/null
+++ b/test/genomecov/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,
diff --git a/test/genomecov/three_blocks_nomatch.bed b/test/genomecov/three_blocks_nomatch.bed
new file mode 100644
index 0000000000000000000000000000000000000000..1835260e64f3ed3770b044ffe587c756f8ef85de
--- /dev/null
+++ b/test/genomecov/three_blocks_nomatch.bed
@@ -0,0 +1 @@
+chr1 10 60 three_blocks_nomatch 0 + 0 0 0 3 10,10,10, 0,20,40,
diff --git a/test/genomecov/two_blocks.sam b/test/genomecov/two_blocks.sam
new file mode 100644
index 0000000000000000000000000000000000000000..a28928abaf6174219c349eebd9b4fcab26ac97da
--- /dev/null
+++ b/test/genomecov/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
\ No newline at end of file
diff --git a/test/intersect/one_block.sam b/test/intersect/one_block.sam
new file mode 100644
index 0000000000000000000000000000000000000000..83041cf531ddf8ca5c02e3175509fa983953d9f0
--- /dev/null
+++ b/test/intersect/one_block.sam
@@ -0,0 +1,3 @@
+@HD VN:1.0 GO:none SO:coordinate
+@SQ SN:chr1 LN:249250621
+one_blocks 16 chr1 1 40 30M * 0 0 GAAGGCCACCGCCGCGGTTATTTTCCTTCA CCCDDB?=FJIIJIGFJIJHIJJJJJJJJI MD:Z:50
diff --git a/test/intersect/test-intersect.sh b/test/intersect/test-intersect.sh
index bbc0cbee9af73fbe47112596f3ed4aac25c286a5..ac12faa159dc1e9a873c5e7cf1f1ee344bb17a79 100644
--- a/test/intersect/test-intersect.sh
+++ b/test/intersect/test-intersect.sh
@@ -190,6 +190,68 @@ rm obs exp
# -split #
###########################################################
###########################################################
+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
+##################################################################
+# Test three blocks matches BED without -split
+##################################################################
+echo " intersect.t17...\c"
+echo \
+"three_blocks 16 chr1 1 40 10M10N10M10N10M * 0 0 GAAGGCCACCGCCGCGGTTATTTTCCTTCA CCCDDB?=FJIIJIGFJIJHIJJJJJJJJI MD:Z:50" > exp
+$BT intersect -abam three_blocks.bam -b three_blocks_nomatch.bed | samtools view - > obs
+check obs exp
+rm obs exp
+
+##################################################################
+# Test three blocks does not match BED with -split
+##################################################################
+echo " intersect.t18...\c"
+touch exp
+$BT intersect -abam three_blocks.bam -b three_blocks_nomatch.bed -split | samtools view - > obs
+check obs exp
+rm obs exp
+
+##################################################################
+# Test three blocks matches BED with -split
+##################################################################
+echo " intersect.t19...\c"
+echo \
+"three_blocks 16 chr1 1 40 10M10N10M10N10M * 0 0 GAAGGCCACCGCCGCGGTTATTTTCCTTCA CCCDDB?=FJIIJIGFJIJHIJJJJJJJJI MD:Z:50" > exp
+$BT intersect -abam three_blocks.bam -b three_blocks_match.bed -split | samtools view - > obs
+check obs exp
+rm obs exp
+
+##################################################################
+# Test three blocks does not match BED with -split and -s
+# BAM os -, BED is +
+##################################################################
+echo " intersect.t20...\c"
+touch exp
+$BT intersect -abam three_blocks.bam -b three_blocks_match.bed -split -s | samtools view - > obs
+check obs exp
+rm obs exp
+
+##################################################################
+# Test three blocks match BED that overlap 1bp with -split
+##################################################################
+echo " intersect.t21...\c"
+echo \
+"three_blocks 16 chr1 1 40 10M10N10M10N10M * 0 0 GAAGGCCACCGCCGCGGTTATTTTCCTTCA CCCDDB?=FJIIJIGFJIJHIJJJJJJJJI MD:Z:50" > exp
+$BT intersect -abam three_blocks.bam -b three_blocks_match_1bp.bed -split | samtools view - > obs
+check obs exp
+rm obs exp
+
+################################################################################
+# Test three blocks does not match BED that overlap 1bp with -split and -f 0.1
+################################################################################
+echo " intersect.t22...\c"
+touch exp
+$BT intersect -abam three_blocks.bam -b three_blocks_match_1bp.bed -split -f 0.1 | samtools view - > obs
+check obs exp
+rm obs exp
+
+rm *.bam
\ No newline at end of file
diff --git a/test/intersect/three_blocks.sam b/test/intersect/three_blocks.sam
new file mode 100644
index 0000000000000000000000000000000000000000..6e3bc601a7135401ddcadcff667be01bbd30a62a
--- /dev/null
+++ b/test/intersect/three_blocks.sam
@@ -0,0 +1,3 @@
+@HD VN:1.0 GO:none SO:coordinate
+@SQ SN:chr1 LN:249250621
+three_blocks 16 chr1 1 40 10M10N10M10N10M * 0 0 GAAGGCCACCGCCGCGGTTATTTTCCTTCA CCCDDB?=FJIIJIGFJIJHIJJJJJJJJI MD:Z:50
diff --git a/test/intersect/three_blocks_match.bed b/test/intersect/three_blocks_match.bed
new file mode 100644
index 0000000000000000000000000000000000000000..33123c2f69f08c6dce7cf093cb07be44bb5f9113
--- /dev/null
+++ b/test/intersect/three_blocks_match.bed
@@ -0,0 +1 @@
+chr1 0 50 three_blocks_match 0 + 0 0 0 3 10,10,10, 0,20,40,
diff --git a/test/intersect/three_blocks_match_1bp.bed b/test/intersect/three_blocks_match_1bp.bed
new file mode 100644
index 0000000000000000000000000000000000000000..de8b10d2b4a259eebdf71d7995d930ee23c69af6
--- /dev/null
+++ b/test/intersect/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,
diff --git a/test/intersect/three_blocks_nomatch.bed b/test/intersect/three_blocks_nomatch.bed
new file mode 100644
index 0000000000000000000000000000000000000000..1835260e64f3ed3770b044ffe587c756f8ef85de
--- /dev/null
+++ b/test/intersect/three_blocks_nomatch.bed
@@ -0,0 +1 @@
+chr1 10 60 three_blocks_nomatch 0 + 0 0 0 3 10,10,10, 0,20,40,
diff --git a/test/intersect/two_blocks.sam b/test/intersect/two_blocks.sam
new file mode 100644
index 0000000000000000000000000000000000000000..6f19dcf93903dc6eed1548121bdb11bc0e9625cc
--- /dev/null
+++ b/test/intersect/two_blocks.sam
@@ -0,0 +1,3 @@
+@HD VN:1.0 GO:none SO:coordinate
+@SQ SN:chr1 LN:249250621
+two_blocks 16 chr1 1 40 15M10N15M * 0 0 GAAGGCCACCGCCGCGGTTATTTTCCTTCA CCCDDB?=FJIIJIGFJIJHIJJJJJJJJI MD:Z:50
\ No newline at end of file
diff --git a/test/test.sh b/test/test.sh
index da6b533b536defd3d2094934acab6c0ebe767bfb..9c287896ec6b51523fe268a95ced2d0d2c1a8d04 100644
--- a/test/test.sh
+++ b/test/test.sh
@@ -3,6 +3,20 @@ cd general
sh test-general.sh
cd ..
+echo " Testing bedtools bed12tobed6:"
+cd bed12tobed6
+sh test-bed12tobed6.sh
+cd ..
+
+echo " Testing bedtools bamtobed:"
+cd bamtobed
+sh test-bamtobed.sh
+cd ..
+
+echo " Testing bedtools genomecov:"
+cd genomecov
+sh test-genomecov.sh
+cd ..
echo " Testing bedtools intersect:"
cd intersect