diff --git a/src/intersectFile/Makefile b/src/intersectFile/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..0b37027a789f65e7f584e42e8d359653e3e129fa
--- /dev/null
+++ b/src/intersectFile/Makefile
@@ -0,0 +1,43 @@
+UTILITIES_DIR = ../utils/
+OBJ_DIR = ../../obj/
+BIN_DIR = ../../bin/
+
+# -------------------
+# define our includes
+# -------------------
+INCLUDES = -I$(UTILITIES_DIR)/Contexts/ \
+ -I$(UTILITIES_DIR)/general/ \
+ -I$(UTILITIES_DIR)/fileType/ \
+ -I$(UTILITIES_DIR)/gzstream/ \
+ -I$(UTILITIES_DIR)/GenomeFile/ \
+ -I$(UTILITIES_DIR)/BamTools/include \
+ -I$(UTILITIES_DIR)/BlockedIntervals \
+ -I$(UTILITIES_DIR)/BamTools-Ancillary \
+ -I$(UTILITIES_DIR)/FileRecordTools/ \
+ -I$(UTILITIES_DIR)/FileRecordTools/FileReaders/ \
+ -I$(UTILITIES_DIR)/FileRecordTools/Records/ \
+ -I$(UTILITIES_DIR)/NewChromsweep \
+ -I$(UTILITIES_DIR)/BinTree \
+ -I$(UTILITIES_DIR)/version/
+
+# ----------------------------------
+# define our source and object files
+# ----------------------------------
+SOURCES= intersectMain.cpp intersectFile.cpp intersectFile.h
+OBJECTS= intersectMain.o intersectFile.o
+BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
+PROGRAM= intersectFile
+
+all: $(BUILT_OBJECTS)
+
+.PHONY: all
+
+$(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+ @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
+
+clean:
+ @echo "Cleaning up."
+ @rm -f $(OBJ_DIR)/intersectMain.o $(OBJ_DIR)/intersectFile.o
+
+.PHONY: clean
diff --git a/src/intersectFile/intersectFile.cpp b/src/intersectFile/intersectFile.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..914be97dea108bf69371007697d3e7512f80bea2
--- /dev/null
+++ b/src/intersectFile/intersectFile.cpp
@@ -0,0 +1,130 @@
+/*****************************************************************************
+ intersectFile.cpp
+
+ (c) 2009 - Aaron Quinlan
+ Hall Laboratory
+ Department of Biochemistry and Molecular Genetics
+ University of Virginia
+ aaronquinlan@gmail.com
+
+ Licenced under the GNU General Public License 2.0 license.
+******************************************************************************/
+
+#include "intersectFile.h"
+#include "Context.h"
+#include "FileRecordMgr.h"
+#include "NewChromsweep.h"
+#include "BinTree.h"
+#include "RecordOutputMgr.h"
+
+
+FileIntersect::FileIntersect(Context *context)
+: _context(context),
+ _blockMgr(NULL),
+ _recordOutputMgr(NULL)
+{
+ _blockMgr = new BlockMgr();
+ _blockMgr->setContext(context);
+ _recordOutputMgr = new RecordOutputMgr();
+}
+
+FileIntersect::~FileIntersect(void) {
+ if (_blockMgr != NULL) {
+ delete _blockMgr;
+ _blockMgr = NULL;
+ }
+ delete _recordOutputMgr;
+}
+
+void FileIntersect::processHits(RecordKeyList &hits) {
+ if (hits.getKey()->getType() == FileRecordTypeChecker::BAM_RECORD_TYPE) {
+ RecordKeyList blockList(hits.getKey());
+ bool deleteBlocks = false;
+ _blockMgr->getBlocks(blockList, deleteBlocks);
+ _recordOutputMgr->printRecord(hits, &blockList);
+ if (deleteBlocks) {
+ _blockMgr->deleteBlocks(blockList);
+ }
+ return;
+ }
+ _recordOutputMgr->printRecord(hits);
+}
+
+bool FileIntersect::intersectFiles()
+{
+ if (_context->getSortedInput()) {
+ return processSortedFiles();
+ }
+ return processUnsortedFiles();
+}
+
+bool FileIntersect::processSortedFiles()
+{
+ // use the chromsweep algorithm to detect overlaps on the fly.
+ NewChromSweep sweep(_context);
+
+ if (!sweep.init()) {
+ return false;
+ }
+ if (!_recordOutputMgr->init(_context)) {
+ return false;
+ }
+
+ RecordKeyList hitSet;
+ while (sweep.next(hitSet)) {
+ if (_context->getObeySplits()) {
+ RecordKeyList keySet(hitSet.getKey());
+ RecordKeyList resultSet(hitSet.getKey());
+ _blockMgr->findBlockedOverlaps(keySet, hitSet, resultSet);
+ processHits(resultSet);
+ } else {
+ processHits(hitSet);
+ }
+ }
+ return true;
+}
+
+bool FileIntersect::processUnsortedFiles()
+{
+ const QuickString &databaseFilename = _context->getDatabaseFileName();
+ BinTree *binTree = new BinTree(_context->getDatabaseFileIdx(), _context);
+
+ FileRecordMgr *queryFRM = new FileRecordMgr(_context->getQueryFileIdx(), _context);
+ if (!queryFRM->open()) {
+ return false;
+ }
+
+ if (!binTree->loadDB()) {
+ fprintf(stderr, "Error: Unable to load database file %s.\n", databaseFilename.c_str());
+ delete binTree;
+ exit(1);
+ }
+
+
+ _context->determineOutputType();
+ _recordOutputMgr->init(_context);
+
+ while (!queryFRM->eof()) {
+ Record *queryRecord = queryFRM->allocateAndGetNextRecord();
+ if (queryRecord == NULL) {
+ continue;
+ }
+ RecordKeyList hitSet(queryRecord);
+ binTree->getHits(queryRecord, hitSet);
+ if (_context->getObeySplits()) {
+ RecordKeyList keySet(hitSet.getKey());
+ RecordKeyList resultSet;
+ _blockMgr->findBlockedOverlaps(keySet, hitSet, resultSet);
+ processHits(resultSet);
+ } else {
+ processHits(hitSet);
+ }
+ queryFRM->deleteRecord(queryRecord);
+ }
+ queryFRM->close();
+
+ //clean up.
+ delete queryFRM;
+ delete binTree;
+ return true;
+}
diff --git a/src/intersectFile/intersectFile.h b/src/intersectFile/intersectFile.h
new file mode 100644
index 0000000000000000000000000000000000000000..3922aa9120ac05f9046d1f58b4ce77d3ccf4cf48
--- /dev/null
+++ b/src/intersectFile/intersectFile.h
@@ -0,0 +1,46 @@
+/*****************************************************************************
+ intersectFile.h
+
+ (c) 2009 - Aaron Quinlan
+ Hall Laboratory
+ Department of Biochemistry and Molecular Genetics
+ University of Virginia
+ aaronquinlan@gmail.com
+
+ Licenced under the GNU General Public License 2.0 license.
+******************************************************************************/
+#ifndef INTERSECTFILE_H
+#define INTERSECTFILE_H
+
+using namespace std;
+
+#include "RecordKeyList.h"
+
+using namespace std;
+
+class Context;
+class BlockMgr;
+class RecordOutputMgr;
+
+class FileIntersect {
+
+public:
+ FileIntersect(Context *context);
+ ~FileIntersect(void);
+
+ bool intersectFiles();
+
+private:
+ Context *_context;
+ Record *_queryRec;
+ Record *_databaseRec;
+ BlockMgr *_blockMgr;
+ RecordOutputMgr *_recordOutputMgr;
+
+ void processHits(RecordKeyList &hits);
+ bool processSortedFiles();
+ bool processUnsortedFiles();
+
+};
+
+#endif /* INTERSECTFILE_H */
diff --git a/src/intersectFile/intersectMain.cpp b/src/intersectFile/intersectMain.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..030d33a854b577ead71aba798d95b85c2320f2f3
--- /dev/null
+++ b/src/intersectFile/intersectMain.cpp
@@ -0,0 +1,119 @@
+/*****************************************************************************
+ intersectMain.cpp
+
+ (c) 2009 - Aaron Quinlan
+ Hall Laboratory
+ Department of Biochemistry and Molecular Genetics
+ University of Virginia
+ aaronquinlan@gmail.com
+
+ Licenced under the GNU General Public License 2.0 license.
+******************************************************************************/
+using namespace std;
+
+#include "intersectFile.h"
+#include "version.h"
+#include "Context.h"
+
+// define our program name
+#define PROGRAM_NAME "bedtools intersect"
+
+void intersect_help(void);
+
+int intersect_main(int argc, char* argv[]) {
+
+ Context *context = new Context();
+ context->parseCmdArgs(argc, argv, 1);
+ if (!context->isValidState()) {
+ fprintf(stderr, "%s\n", context->getErrorMsg().c_str());
+ intersect_help();
+ return 0;
+ }
+
+ FileIntersect *fileIntersect = new FileIntersect(context);
+
+ bool retVal = fileIntersect->intersectFiles();
+ delete fileIntersect;
+ delete context;
+ return retVal ? 0 : 1;
+}
+
+void intersect_help(void) {
+
+ cerr << "\nTool: bedtools intersect (aka intersectBed)" << endl;
+ cerr << "Version: " << VERSION << "\n";
+ cerr << "Summary: Report overlaps between two feature files." << endl << endl;
+
+ cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf>" << endl << endl;
+
+ cerr << "Options: " << endl;
+
+ cerr << "\t-abam\t" << "The A input file is in BAM format. Output will be BAM as well." << endl << endl;
+
+ cerr << "\t-ubam\t" << "Write uncompressed BAM output. Default writes compressed BAM." << endl << endl;
+
+ cerr << "\t-bed\t" << "When using BAM input (-abam), write output as BED. The default" << endl;
+ cerr << "\t\tis to write output in BAM when using -abam." << endl << endl;
+
+ cerr << "\t-wa\t" << "Write the original entry in A for each overlap." << endl << endl;
+
+ cerr << "\t-wb\t" << "Write the original entry in B for each overlap." << endl;
+ cerr << "\t\t- Useful for knowing _what_ A overlaps. Restricted by -f and -r." << endl << endl;
+
+ cerr << "\t-loj\t" << "Perform a \"left outer join\". That is, for each feature in A" << endl;
+ cerr << "\t\treport each overlap with B. If no overlaps are found, " << endl;
+ cerr << "\t\treport a NULL feature for B." << endl << endl;
+
+ cerr << "\t-wo\t" << "Write the original A and B entries plus the number of base" << endl;
+ cerr << "\t\tpairs of overlap between the two features." << endl;
+ cerr << "\t\t- Overlaps restricted by -f and -r." << endl;
+ cerr << "\t\t Only A features with overlap are reported." << endl << endl;
+
+ cerr << "\t-wao\t" << "Write the original A and B entries plus the number of base" << endl;
+ cerr << "\t\tpairs of overlap between the two features." << endl;
+ cerr << "\t\t- Overlapping features restricted by -f and -r." << endl;
+ cerr << "\t\t However, A features w/o overlap are also reported" << endl;
+ cerr << "\t\t with a NULL B feature and overlap = 0." << endl << endl;
+
+ cerr << "\t-u\t" << "Write the original A entry _once_ if _any_ overlaps found in B." << endl;
+ cerr << "\t\t- In other words, just report the fact >=1 hit was found." << endl;
+ cerr << "\t\t- Overlaps restricted by -f and -r." << endl << endl;
+
+ cerr << "\t-c\t" << "For each entry in A, report the number of overlaps with B." << endl;
+ cerr << "\t\t- Reports 0 for A entries that have no overlap with B." << endl;
+ cerr << "\t\t- Overlaps restricted by -f and -r." << endl << endl;
+
+ cerr << "\t-v\t" << "Only report those entries in A that have _no overlaps_ with B." << endl;
+ cerr << "\t\t- Similar to \"grep -v\" (an homage)." << endl << endl;
+
+ cerr << "\t-f\t" << "Minimum overlap required as a fraction of A." << endl;
+ cerr << "\t\t- Default is 1E-9 (i.e., 1bp)." << endl;
+ cerr << "\t\t- FLOAT (e.g. 0.50)" << endl << endl;
+
+ cerr << "\t-r\t" << "Require that the fraction overlap be reciprocal for A and B." << endl;
+ cerr << "\t\t- In other words, if -f is 0.90 and -r is used, this requires" << endl;
+ cerr << "\t\t that B overlap 90% of A and A _also_ overlaps 90% of B." << endl << endl;
+
+ cerr << "\t-s\t" << "Require same strandedness. That is, only report hits in B" << endl;
+ cerr << "\t\tthat overlap A on the _same_ strand." << endl;
+ cerr << "\t\t- By default, overlaps are reported without respect to strand." << endl << endl;
+
+ cerr << "\t-S\t" << "Require different strandedness. That is, only report hits in B" << endl;
+ cerr << "\t\tthat overlap A on the _opposite_ strand." << endl;
+ cerr << "\t\t- By default, overlaps are reported without respect to strand." << endl << endl;
+
+ cerr << "\t-split\t" << "Treat \"split\" BAM or BED12 entries as distinct BED intervals." << endl << endl;
+
+ cerr << "\t-sorted\t" << "Use the \"chromsweep\" algorithm for sorted (-k1,1 -k2,2n) input" << endl << endl;
+
+ cerr << "\t-header\t" << "Print the header from the A file prior to results." << endl << endl;
+
+ cerr << "Notes: " << endl;
+ cerr << "\t(1) When a BAM file is used for the A file, the alignment is retained if overlaps exist," << endl;
+ cerr << "\tand exlcuded if an overlap cannot be found. If multiple overlaps exist, they are not" << endl;
+ cerr << "\treported, as we are only testing for one or more overlaps." << endl << endl;
+
+ // end the program here
+ exit(1);
+
+}