diff --git a/Makefile b/Makefile
index e7b741ab8e5464b0bbb33bcba62e66fda56eb9fd..d61800288ed348916f91fa143c665f5303bd7b06 100755
--- a/Makefile
+++ b/Makefile
@@ -21,23 +21,27 @@ export CXX ?= g++
# define our source subdirectories
SUBDIRS = $(SRC_DIR)/closestBed $(SRC_DIR)/complementBed $(SRC_DIR)/coverageBed $(SRC_DIR)/intersectBed $(SRC_DIR)/mergeBed $(SRC_DIR)/genomeCoverageBed $(SRC_DIR)/fastaFromBed $(SRC_DIR)/sortBed $(SRC_DIR)/windowBed $(SRC_DIR)/subtractBed $(SRC_DIR)/linksBed $(SRC_DIR)/peIntersectBed
-UTIL_SUBDIRS = $(SRC_DIR)/utils/bedFile $(SRC_DIR)/utils/sequenceUtilities
+UTIL_SUBDIRS = $(SRC_DIR)/utils/lineFileUtilities $(SRC_DIR)/utils/bedFile $(SRC_DIR)/utils/bedFilePE $(SRC_DIR)/utils/sequenceUtilities
+
all:
@echo "Building BEDTools:"
@echo "========================================================="
- @for dir in $(SUBDIRS); do \
+
+ @for dir in $(UTIL_SUBDIRS); do \
echo "- Building in $$dir"; \
$(MAKE) --no-print-directory -C $$dir; \
echo ""; \
done
- @for dir in $(UTIL_SUBDIRS); do \
+ @for dir in $(SUBDIRS); do \
echo "- Building in $$dir"; \
$(MAKE) --no-print-directory -C $$dir; \
echo ""; \
done
+
+
.PHONY: all
clean:
diff --git a/bin/genomeCoverageBed b/bin/genomeCoverageBed
index 36424f979729f495a8e41a1ebf15e0bf07b85726..2d9842ec848426c8eee531eae3f90230a55f34d6 100755
Binary files a/bin/genomeCoverageBed and b/bin/genomeCoverageBed differ
diff --git a/obj/genomeCoverageBed.o b/obj/genomeCoverageBed.o
index a17a58acf05989b004bffdd3e3e8ee54d36406e1..980382d644a13ca8af1d6fa624c2a82e66f9a4d7 100644
Binary files a/obj/genomeCoverageBed.o and b/obj/genomeCoverageBed.o differ
diff --git a/obj/genomeCoverageMain.o b/obj/genomeCoverageMain.o
index eccf14ad276152df0d8bbb5b84ac921a0835bc62..45bb001699b15eeb5c67be2d28f54d226b9bba21 100644
Binary files a/obj/genomeCoverageMain.o and b/obj/genomeCoverageMain.o differ
diff --git a/src/fastaFromBed/Makefile b/src/fastaFromBed/Makefile
index 3b703f2d9b7912ae7c6b4f2c6609da732474efb3..06e88fba07f018be447ff66dbf7d22226b7f0806 100755
--- a/src/fastaFromBed/Makefile
+++ b/src/fastaFromBed/Makefile
@@ -38,8 +38,7 @@ $(EXT_OBJECTS):
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/sequenceUtilities/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
-
-
+
clean:
@echo "Cleaning up."
@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
diff --git a/src/genomeCoverageBed/genomeCoverageBed.cpp b/src/genomeCoverageBed/genomeCoverageBed.cpp
index 8e3d899abb91127ef3f070fae99929778774f612..eeaccb819e854430e2084e27bb36576bf0e2da33 100755
--- a/src/genomeCoverageBed/genomeCoverageBed.cpp
+++ b/src/genomeCoverageBed/genomeCoverageBed.cpp
@@ -117,6 +117,9 @@ void BedCoverage::CoverageBeds() {
depth += this->chromCov[chrom][pos];
this->chromCov[chrom][pos] = depth;
}
+ else {
+ this->chromCov[chrom][pos] = depth;
+ }
// report the depth for this position.
cout << chrom << "\t" << pos+1 << "\t" << this->chromCov[chrom][pos] << endl;
diff --git a/src/genomeCoverageBed/genomeCoverageMain.cpp b/src/genomeCoverageBed/genomeCoverageMain.cpp
index b64cbacf80a620f1a06d22233c2738fa56b5b313..d31d338c7bfa4d9801cdea9f38e276917b379b80 100755
--- a/src/genomeCoverageBed/genomeCoverageMain.cpp
+++ b/src/genomeCoverageBed/genomeCoverageMain.cpp
@@ -62,10 +62,10 @@ int main(int argc, char* argv[]) {
eachBase = true;
i++;
}
- else if(PARAMETER_CHECK("-s", 2, parameterLength)) {
- startSites = true;
- i++;
- }
+ //else if(PARAMETER_CHECK("-s", 2, parameterLength)) {
+ // startSites = true;
+ // i++;
+ //}
else if(PARAMETER_CHECK("-max", 4, parameterLength)) {
max = atoi(argv[i + 1]);
i++;
@@ -108,7 +108,7 @@ void ShowHelp(void) {
cerr << "OPTIONS: " << endl;
cerr << "\t" << "-d\t\t\t" << "Report the depth at each genome position." << endl << "\t\t\t\tDefault behavior is to report a histogram." << endl << endl;
- cerr << "\t" << "-s \t\t\t" << "Report depth based on start sites." << endl << endl;
+ // cerr << "\t" << "-s \t\t\t" << "Report depth based on start sites." << endl << endl;
cerr << "\t" << "-max\t\t\t" << "Combine all positions with a depth > max into a single bin in the histogram." << endl << endl;
cerr << "NOTES: " << endl;
cerr << "\tThe genome file should tab delimited and structured as follows: <chr><TAB><size>. For example, Mus musculus:" << endl;
diff --git a/src/intersectBed/13.out b/src/intersectBed/13.out
new file mode 100644
index 0000000000000000000000000000000000000000..f8dd81d3828331d4180c0af35ac655eab66b1bca
--- /dev/null
+++ b/src/intersectBed/13.out
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diff --git a/src/intersectBed/17.out b/src/intersectBed/17.out
new file mode 100644
index 0000000000000000000000000000000000000000..f8dd81d3828331d4180c0af35ac655eab66b1bca
--- /dev/null
+++ b/src/intersectBed/17.out
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diff --git a/src/intersectBed/chr1_snp129.bed b/src/intersectBed/chr1_snp129.bed
new file mode 100644
index 0000000000000000000000000000000000000000..97fe24a97322bd34f64c612994dd90747aa734a2
--- /dev/null
+++ b/src/intersectBed/chr1_snp129.bed
@@ -0,0 +1,36707 @@
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diff --git a/src/intersectBed/new.out b/src/intersectBed/new.out
new file mode 100644
index 0000000000000000000000000000000000000000..f8dd81d3828331d4180c0af35ac655eab66b1bca
--- /dev/null
+++ b/src/intersectBed/new.out
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+chr1 4968069 4968070 rs10915310 0 +
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+chr1 4968104 4968105 rs10799151 0 +
+chr1 4968104 4968105 rs10799151 0 +
+chr1 4968192 4968193 rs12691487 0 +
+chr1 4968192 4968193 rs12691487 0 +
+chr1 4968192 4968193 rs55969666 0 +
+chr1 4968192 4968196 rs55969666 0 +
+chr1 4968621 4968622 rs2100728 0 +
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+chr1 4969530 4969531 rs2878167 0 -
+chr1 4969530 4969531 rs2878167 0 -
+chr1 4969530 4969531 rs60284801 0 +
+chr1 4969530 4969538 rs60284801 0 +
+chr1 4969531 4969532 rs60284801 0 +
+chr1 4969533 4969534 rs60284801 0 +
+chr1 4969534 4969535 rs60284801 0 +
+chr1 4969531 4969532 rs2878166 0 -
+chr1 4969531 4969532 rs2878166 0 -
+chr1 4969533 4969534 rs2334264 0 -
+chr1 4969533 4969534 rs2334264 0 -
+chr1 4969534 4969535 rs2878165 0 -
+chr1 4969534 4969535 rs2878165 0 -
+chr1 4970266 4970267 rs10915312 0 +
+chr1 4970522 4970523 rs12045336 0 +
+chr1 4971332 4971333 rs34815468 0 +
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+chr1 4971347 4971348 rs10915313 0 +
+chr1 4971620 4971621 rs61766695 0 +
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+chr1 4976181 4976182 rs10915314 0 +
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+chr1 4980925 4980926 rs10915317 0 +
+chr1 4981032 4981033 rs898337 0 -
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+chr1 4987921 4987922 rs1459765 0 -
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+chr1 4997394 4997395 rs7538599 0 +
+chr1 4997880 4997881 rs1157959 0 -
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+chr1 4998122 4998123 rs12121943 0 +
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diff --git a/src/peIntersectBed/peIntersectBed.cpp b/src/peIntersectBed/peIntersectBed.cpp
index d4d6b15472c3a7b53e2e685f518aa1e92a495d52..4228f1a54837b7dea1694a7f258c5dddb7963d5c 100755
--- a/src/peIntersectBed/peIntersectBed.cpp
+++ b/src/peIntersectBed/peIntersectBed.cpp
@@ -179,6 +179,7 @@ void BedIntersectPE::FindSpanningOverlaps(BEDPE &a, vector<BED> &hits, string &t
int s = max(spanStart, h->start);
int e = min(spanEnd, h->end);
+ // overlap if s < e
if (s < e) {
// is there enough overlap (default ~ 1bp)
diff --git a/src/peIntersectBed/peIntersectMain.cpp b/src/peIntersectBed/peIntersectMain.cpp
index 93bdbdb823c70cd0a373687c75d209709842ec6a..1d46d937929d572d1db7c315e7b7ba061122a3cd 100755
--- a/src/peIntersectBed/peIntersectMain.cpp
+++ b/src/peIntersectBed/peIntersectMain.cpp
@@ -25,6 +25,7 @@ int main(int argc, char* argv[]) {
float overlapFraction = 1E-9;
string searchType = "either";
+ // flags to track parameters
bool haveBedA = false;
bool haveBedB = false;
bool haveSearchType = false;
@@ -81,6 +82,7 @@ int main(int argc, char* argv[]) {
}
}
+
// make sure we have both input files
if (!haveBedA || !haveBedB) {
cerr << endl << "*****" << endl << "*****ERROR: Need -a and -b files. " << endl << "*****" << endl;
diff --git a/src/utils/bedFile/Makefile b/src/utils/bedFile/Makefile
index 900d6a422ae15f70bcdda37efb5857199ef24e11..41a166865a358cbe0e3d07fc8bdd01620d8ad548 100755
--- a/src/utils/bedFile/Makefile
+++ b/src/utils/bedFile/Makefile
@@ -23,7 +23,7 @@ $(BUILT_OBJECTS): $(SOURCES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
$(EXT_OBJECTS):
- @$(MAKE) --no-print-directory -C $(INCLUDES)
+ @$(MAKE) --no-print-directory -C -W $(INCLUDES)
clean:
@echo "Cleaning up."
diff --git a/src/utils/bedFile/bedFile.cpp b/src/utils/bedFile/bedFile.cpp
index fbdf44f38ba03c0daaa8bdb57e9620a2d11aa82e..db1c7fa8582ae2f7bb1a8a2552b3530d37713425 100755
--- a/src/utils/bedFile/bedFile.cpp
+++ b/src/utils/bedFile/bedFile.cpp
@@ -16,19 +16,23 @@
static int binOffsetsExtended[] =
{4096+512+64+8+1, 512+64+8+1, 64+8+1, 8+1, 1, 0};
-//static int binOffsets[] = {512+64+8+1, 64+8+1, 8+1, 1, 0};
-#define _binFirstShift 17/* How much to shift to get to finest bin. */
-#define _binNextShift 3/* How much to shift to get to next larger bin. */
+
+
+#define _binFirstShift 17 /* How much to shift to get to finest bin. */
+#define _binNextShift 3 /* How much to shift to get to next larger bin. */
+// return the amount of overlap between two features. Negative if none.
int overlaps(const int aS, const int aE, const int bS, const int bE) {
return min(aE, bE) - max(aS, bS);
}
+
bool leftOf(const int a, const int b) {
return (a < b);
}
+// return the lesser of two values.
int min(const int a, int b) {
if (a <= b) {
return a;
@@ -38,6 +42,7 @@ int min(const int a, int b) {
}
}
+// return the greater of two values.
int max(const int a, int b) {
if (a >= b) {
return a;
@@ -47,9 +52,6 @@ int max(const int a, int b) {
}
}
-//************************************************
-// Exception checking
-//************************************************
static int getBin(int start, int end)
/*
@@ -64,14 +66,15 @@ static int getBin(int start, int end)
int startBin = start, endBin = end-1, i;
startBin >>= _binFirstShift;
endBin >>= _binFirstShift;
- for (i=0; i<6; ++i)
- {
+
+ for (i=0; i<6; ++i) {
if (startBin == endBin) {
return binOffsetsExtended[i] + startBin;
}
startBin >>= _binNextShift;
endBin >>= _binNextShift;
}
+
cerr << "start " << start << ", end " << end << " out of range in findBin (max is 512M)" << endl;
return 0;
}
@@ -129,31 +132,27 @@ bool byChromThenStart(BED const & a, BED const & b){
return false;
};
-void BedFile::binKeeperFind(map<int, vector<BED>, std::less<int> > &bk, const int start, const int end, vector<BED> &hits)
-/*
+
+/*
NOTE: Taken ~verbatim from kent source.
Return a list of all items in binKeeper that intersect range.
- * Free this list with slFreeList. */
-
-{
+ Free this list with slFreeList.
+*/
+void BedFile::binKeeperFind(map<int, vector<BED>, std::less<int> > &bk, const int start, const int end, vector<BED> &hits) {
+
int startBin, endBin;
int i,j;
startBin = (start>>_binFirstShift);
endBin = ((end-1)>>_binFirstShift);
- for (i=0; i<6; ++i)
- {
+ for (i=0; i<6; ++i) {
int offset = binOffsetsExtended[i];
- for (j=(startBin+offset); j<=(endBin+offset); ++j)
- {
+ for (j = (startBin+offset); j <= (endBin+offset); ++j) {
for (vector<BED>::iterator el = bk[j].begin(); el != bk[j].end(); ++el) {
- {
- if (overlaps(el->start, el->end, start, end) > 0)
- {
- hits.push_back(*el);
- }
+ if (overlaps(el->start, el->end, start, end) > 0) {
+ hits.push_back(*el);
}
}
}
@@ -163,27 +162,19 @@ void BedFile::binKeeperFind(map<int, vector<BED>, std::less<int> > &bk, const in
}
-void BedFile::countHits(map<int, vector<BED>, std::less<int> > &bk, const int start, const int end)
-/* Return a list of all items in binKeeper that intersect range.
- * Free this list with slFreeList. */
-{
+void BedFile::countHits(map<int, vector<BED>, std::less<int> > &bk, const int start, const int end) {
int startBin, endBin;
int i,j;
startBin = (start>>_binFirstShift);
endBin = ((end-1)>>_binFirstShift);
- for (i=0; i<6; ++i)
- {
+ for (i=0; i<6; ++i) {
int offset = binOffsetsExtended[i];
- for (j=(startBin+offset); j<=(endBin+offset); ++j)
- {
+ for (j = (startBin+offset); j <= (endBin+offset); ++j) {
for (vector<BED>::iterator el = bk[j].begin(); el != bk[j].end(); ++el) {
- {
- if (overlaps(el->start, el->end, start, end) > 0)
- {
- el->count++;
- }
+ if (overlaps(el->start, el->end, start, end) > 0) {
+ el->count++;
}
}
}
@@ -350,6 +341,7 @@ void BedFile::loadBedFileIntoMap() {
}
}
+
void BedFile::loadBedFileIntoMapNoBin() {
string bedLine;