Added jaccard w/ -split and unit tests. Fixed Bam input as bam output bug,...

Added jaccard w/ -split and unit tests. Fixed Bam input as bam output bug, added unit test in sample.

src/jaccard/Jaccard.cpp

+/*****************************************************************************
+  Jaccard.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 "Jaccard.h"
+#include "BlockMgr.h"
+#include "NewChromsweep.h"
+
+Jaccard::Jaccard(ContextJaccard *context)
+: _context(context),
+  _intersectionVal(0),
+  _unionVal(0),
+  _numIntersections(0)
+{
+	_blockMgr = new BlockMgr(_context->getOverlapFraction(), _context->getReciprocal());
+}
+
+Jaccard::~Jaccard(void) {
+	delete _blockMgr;
+	_blockMgr = NULL;
+}
+
+bool Jaccard::calculate() {
+
+	if (!getIntersectionAndUnion()) {
+		return false;
+	}
+
+	// header
+	cout << "intersection\tunion-intersection\tjaccard\tn_intersections" << endl;
+
+	unsigned long adjustedUnion = _unionVal - _intersectionVal;
+
+	cout << _intersectionVal << "\t" << adjustedUnion << "\t" <<
+			(float) _intersectionVal / (float)adjustedUnion << "\t" << _numIntersections << endl;
+	return true;
+}
+
+bool Jaccard::getIntersectionAndUnion() {
+	NewChromSweep sweep(_context);
+	if (!sweep.init()) {
+		return false;
+	}
+	RecordKeyList hitSet;
+	while (sweep.next(hitSet)) {
+		if (_context->getObeySplits()) {
+			RecordKeyList keySet(hitSet.getKey());
+			RecordKeyList resultSet(hitSet.getKey());
+			_blockMgr->findBlockedOverlaps(keySet, hitSet, resultSet);
+			_intersectionVal += getTotalIntersection(&resultSet);
+		} else {
+			_intersectionVal += getTotalIntersection(&hitSet);
+		}
+	}
+
+	sweep.closeOut();
+	unsigned long queryUnion = sweep.getQueryTotalRecordLength();
+	unsigned long dbUnion = sweep.getDatabaseTotalRecordLength();
+
+	_unionVal = queryUnion + dbUnion;
+	return true;
+}
+
+unsigned long Jaccard::getTotalIntersection(RecordKeyList *recList)
+{
+	unsigned long intersection = 0;
+	const Record *key = recList->getKey();
+	int keyStart = key->getStartPos();
+	int keyEnd = key->getEndPos();
+
+	int hitIdx = 0;
+	for (RecordKeyList::const_iterator_type iter = recList->begin(); iter != recList->end(); iter = recList->next()) {
+		const Record *currRec = iter->value();
+		int maxStart = max(currRec->getStartPos(), keyStart);
+		int minEnd = min(currRec->getEndPos(), keyEnd);
+		if (_context->getObeySplits()) {
+			intersection += _blockMgr->getOverlapBases(hitIdx);
+			hitIdx++;
+		} else {
+			intersection += (unsigned long)(minEnd - maxStart);
+		}
+	}
+	_numIntersections += (int)recList->size();
+	return intersection;
+}
+

src/jaccard/jaccard.h → src/jaccard/Jaccard.h

@@ -12,59 +12,28 @@
 #ifndef JACCARD_H
 #define JACCARD_H
 
-#include "bedFile.h"
-#include "chromsweep.h"
-#include "api/BamReader.h"
-#include "api/BamAux.h"
-#include "BlockedIntervals.h"
-#include "BamAncillary.h"
-using namespace BamTools;
-
-
-#include <vector>
-#include <iostream>
-#include <fstream>
-#include <stdlib.h>
-using namespace std;
-
+#include "ContextJaccard.h"
 
+class BlockMgr;
 
 class Jaccard {
 
 public:
 
-    // constructor
-    Jaccard(string bedAFile, string bedBFile, 
-            float overlapFraction, bool reciprocal,
-            bool valueOnly);
+    Jaccard(ContextJaccard *context);
+    ~Jaccard();
 
-    // destructor
-    ~Jaccard(void);
+    bool calculate();
 
 private:
-
-    //------------------------------------------------
-    // private attributes
-    //------------------------------------------------
-    string _bedAFile;
-    string _bedBFile;
-
-    bool  _reciprocal;
-    bool  _valueOnly;
-    float _overlapFraction;
-
-    // instance of a bed file class.
-    BedFile *_bedA, *_bedB;
-
-    //------------------------------------------------
-    // private methods
-    //------------------------------------------------
-    unsigned long GetIntersection(size_t &n_intersections);
-    unsigned long GetUnion();
-    void CalculateJaccard();
-
-    size_t GetTotalIntersection(const BED &a, const vector<BED> &hits);
-
+    ContextJaccard *_context;
+    BlockMgr *_blockMgr;
+    unsigned long _intersectionVal;
+    unsigned long _unionVal;
+    int _numIntersections;
+
+    bool getIntersectionAndUnion();
+    unsigned long getTotalIntersection(RecordKeyList *hits);
 };
 
 #endif /* JACCARD_H */

src/jaccard/Makefile

@@ -5,24 +5,33 @@ BIN_DIR = ../../bin/
 # -------------------
 # define our includes
 # -------------------
-INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
-           -I$(UTILITIES_DIR)/gzstream/ \
-           -I$(UTILITIES_DIR)/genomeFile/ \
-           -I$(UTILITIES_DIR)/lineFileUtilities/ \
-           -I$(UTILITIES_DIR)/fileType/ \
+
+INCLUDES = -I$(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)/BamTools/src \
            -I$(UTILITIES_DIR)/BlockedIntervals \
            -I$(UTILITIES_DIR)/BamTools-Ancillary \
-           -I$(UTILITIES_DIR)/chromsweep \
+           -I$(UTILITIES_DIR)/FileRecordTools/ \
+           -I$(UTILITIES_DIR)/FileRecordTools/FileReaders/ \
+           -I$(UTILITIES_DIR)/FileRecordTools/Records/ \
+           -I$(UTILITIES_DIR)/RecordOutputMgr/ \
+			-I$(UTILITIES_DIR)/KeyListOps/ \
+           -I$(UTILITIES_DIR)/NewChromsweep \
+           -I$(UTILITIES_DIR)/VectorOps \
+           -I$(UTILITIES_DIR)/BinTree \
            -I$(UTILITIES_DIR)/version/
 
 # ----------------------------------
 # define our source and object files
 # ----------------------------------
-SOURCES= jaccardMain.cpp jaccard.cpp jaccard.h
-OBJECTS= jaccardMain.o jaccard.o
+SOURCES= jaccardMain.cpp Jaccard.cpp Jaccard.h
+OBJECTS= jaccardMain.o Jaccard.o
 BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
-PROGRAM= jaccard
+PROGRAM= Jaccard
 
 all: $(BUILT_OBJECTS)
 
@@ -34,6 +43,6 @@ $(BUILT_OBJECTS): $(SOURCES)
 	
 clean:
 	@echo "Cleaning up."
-	@rm -f $(OBJ_DIR)/jaccardMain.o $(OBJ_DIR)/jaccard.o
+	@rm -f $(OBJ_DIR)/jaccardMain.o $(OBJ_DIR)/Jaccard.o
 
 .PHONY: clean

src/jaccard/jaccard.cpp

-/*****************************************************************************
-  jaccard.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 "lineFileUtilities.h"
-#include "jaccard.h"
-
-/************************************
-Helper functions
-************************************/
-size_t Jaccard::GetTotalIntersection(const BED &a, const vector<BED> &hits) 
-{
-
-    size_t intersection = 0;
-    
-    vector<BED>::const_iterator h       = hits.begin();
-    vector<BED>::const_iterator hitsEnd = hits.end();
-    for (; h != hitsEnd; ++h) {
-        CHRPOS s = max(a.start, h->start);
-        CHRPOS e = min(a.end, h->end);
-        intersection += (e - s);
-    }
-    return intersection;
-}
-
-/*
-    Constructor
-*/
-Jaccard::Jaccard(string bedAFile, string bedBFile, 
-                 float overlapFraction, bool reciprocal,
-                 bool valueOnly)
-{
-    _bedAFile            = bedAFile;
-    _bedBFile            = bedBFile;
-    _overlapFraction     = overlapFraction;
-    _reciprocal          = reciprocal;
-    _valueOnly           = valueOnly;
-
-        
-    CalculateJaccard();
-}
-
-
-/*
-    Destructor
-*/
-Jaccard::~Jaccard(void) {
-}
-
-
-unsigned long Jaccard::GetIntersection(size_t &n_intersections) {
-    
-    _bedA = new BedFile(_bedAFile);
-    _bedB = new BedFile(_bedBFile);
-    
-    unsigned long I = 0;
-
-    ChromSweep sweep = ChromSweep(_bedA, _bedB, 
-                                  false, false, 
-                                  _overlapFraction, _reciprocal,
-                                  true, false);
-
-
-    pair<BED, vector<BED> > hit_set;
-    hit_set.second.reserve(10000);
-    while (sweep.Next(hit_set)) {
-        I += GetTotalIntersection(hit_set.first, hit_set.second);
-        n_intersections += hit_set.second.size();
-    }
-    return I;
-}
-
-void Jaccard::CalculateJaccard() {
-
-    size_t n_intersections = 0;
-    unsigned long I = GetIntersection(n_intersections);
-    
-    unsigned long U = _bedA->getTotalFlattenedLength() + \
-                      _bedB->getTotalFlattenedLength();
-    
-    float jaccard_stat = (float) I / ((float) U - (float) I);
-    
-    if (!_valueOnly) {
-        // header
-        cout << "intersection\t"
-           << "union-intersection\t"
-           << "jaccard\t"
-           << "n_intersections"
-           << endl;
-
-        // result
-        cout << I << "\t" 
-           << U - I << "\t"
-           << jaccard_stat << "\t"
-           << n_intersections
-           << endl;
-    }
-    else {
-        cout << jaccard_stat << endl;
-    }
-}
-
-

src/jaccard/jaccardMain.cpp

@@ -9,124 +9,39 @@
 
   Licenced under the GNU General Public License 2.0 license.
 ******************************************************************************/
-#include "jaccard.h"
+#include "Jaccard.h"
 #include "version.h"
 
 using namespace std;
 
-// define our program name
 #define PROGRAM_NAME "bedtools jaccard"
 
-
-// define our parameter checking macro
-#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)
-
-// function declarations
 void jaccard_help(void);
 
 int jaccard_main(int argc, char* argv[]) {
 
-    // our configuration variables
-    bool showHelp = false;
-
-    // input files
-    string bedAFile;
-    string bedBFile;
-
-    // input arguments
-    float overlapFraction = 1E-9;
-
-    bool haveBedA           = false;
-    bool haveBedB           = false;
-    bool haveFraction       = false;
-    bool reciprocalFraction = false;
-    bool valueOnly = false;
-
-    // check to see if we should print out some help
-    if(argc <= 1) showHelp = true;
-
-    for(int i = 1; i < argc; i++) {
-        int parameterLength = (int)strlen(argv[i]);
-
-        if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
-        (PARAMETER_CHECK("--help", 5, parameterLength))) {
-            showHelp = true;
-        }
+    ContextJaccard *context = new ContextJaccard();
+    if (!context->parseCmdArgs(argc, argv, 1) || context->getShowHelp() || !context->isValidState()) {
+    	if (!context->getErrorMsg().empty()) {
+    		cerr << context->getErrorMsg() << endl;
+    	}
+    	jaccard_help();
+    	delete context;
+    	return 0;
     }
+	Jaccard *jaccard = new Jaccard(context);
 
-    if(showHelp) jaccard_help();
-
-    // do some parsing (all of these parameters require 2 strings)
-    for(int i = 1; i < argc; i++) {
-
-        int parameterLength = (int)strlen(argv[i]);
-
-        if(PARAMETER_CHECK("-a", 2, parameterLength)) {
-            if ((i+1) < argc) {
-                haveBedA = true;
-                bedAFile = argv[i + 1];
-                i++;
-            }
-        }
-        else if(PARAMETER_CHECK("-b", 2, parameterLength)) {
-            if ((i+1) < argc) {
-                haveBedB = true;
-                bedBFile = argv[i + 1];
-                i++;
-            }
-        }
-        else if(PARAMETER_CHECK("-f", 2, parameterLength)) {
-            if ((i+1) < argc) {
-                haveFraction = true;
-                overlapFraction = atof(argv[i + 1]);
-                i++;
-            }
-        }
-        else if(PARAMETER_CHECK("-r", 2, parameterLength)) {
-            reciprocalFraction = true;
-        }
-        else if(PARAMETER_CHECK("-valueOnly", 10, parameterLength)) {
-            valueOnly = true;
-        }
-        else {
-            cerr << endl 
-                 << "*****ERROR: Unrecognized parameter: " 
-                 << argv[i] 
-                 << " *****" 
-                 << endl << endl;
-            showHelp = true;
-        }
-    }
-
-    // make sure we have both input files
-    if (!haveBedA || !haveBedB) {
-        cerr << endl << "*****" << endl << "*****ERROR: Need -a and -b files. " << endl << "*****" << endl;
-        showHelp = true;
-    }
-
-    if (reciprocalFraction && !haveFraction) {
-        cerr << endl << "*****" << endl << "*****ERROR: If using -r, you need to define -f." << endl << "*****" << endl;
-        showHelp = true;
-    }
-
-    if (!showHelp) {
-
-        Jaccard *j = new Jaccard(bedAFile, bedBFile,
-                                 overlapFraction, reciprocalFraction,
-                                 valueOnly);
-        delete j;
-        return 0;
-    }
-    else {
-        jaccard_help();
-        return 0;
-    }
+	bool retVal = jaccard->calculate();
+	delete jaccard;
+	delete context;
+	return retVal ? 0 : 1;
 }
 
+
 void jaccard_help(void) {
 
     cerr << "\nTool:    bedtools jaccard (aka jaccard)" << endl;
-    cerr << "Version: " << VERSION << "\n";    
+    cerr << "Version: " << VERSION << "\n";
     cerr << "Summary: Calculate Jaccard statistic b/w two feature files."
          << endl
          << "\t Jaccard is the length of the intersection over the union."
@@ -146,12 +61,122 @@ void jaccard_help(void) {
     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-split\t"        << "Treat \"split\" BAM or BED12 entries as distinct BED intervals." << endl << endl;
+
     cerr << "Notes: " << endl;
-    cerr << "\t(1) Input files must be sorted by chrom, then start position." 
+    cerr << "\t(1) Input files must be sorted by chrom, then start position."
          << endl << endl;
 
     // end the program here
     exit(1);
 
 }
+
+//// define our program name
+//
+//
+//// define our parameter checking macro
+//#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)
+//
+//// function declarations
+//void jaccard_help(void);
+//
+//int jaccard_main(int argc, char* argv[]) {
+//
+//    // our configuration variables
+//    bool showHelp = false;
+//
+//    // input files
+//    string bedAFile;
+//    string bedBFile;
+//
+//    // input arguments
+//    float overlapFraction = 1E-9;
+//
+//    bool haveBedA           = false;
+//    bool haveBedB           = false;
+//    bool haveFraction       = false;
+//    bool reciprocalFraction = false;
+//    bool valueOnly = false;
+//
+//    // check to see if we should print out some help
+//    if(argc <= 1) showHelp = true;
+//
+//    for(int i = 1; i < argc; i++) {
+//        int parameterLength = (int)strlen(argv[i]);
+//
+//        if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
+//        (PARAMETER_CHECK("--help", 5, parameterLength))) {
+//            showHelp = true;
+//        }
+//    }
+//
+//    if(showHelp) jaccard_help();
+//
+//    // do some parsing (all of these parameters require 2 strings)
+//    for(int i = 1; i < argc; i++) {
+//
+//        int parameterLength = (int)strlen(argv[i]);
+//
+//        if(PARAMETER_CHECK("-a", 2, parameterLength)) {
+//            if ((i+1) < argc) {
+//                haveBedA = true;
+//                bedAFile = argv[i + 1];
+//                i++;
+//            }
+//        }
+//        else if(PARAMETER_CHECK("-b", 2, parameterLength)) {
+//            if ((i+1) < argc) {
+//                haveBedB = true;
+//                bedBFile = argv[i + 1];
+//                i++;
+//            }
+//        }
+//        else if(PARAMETER_CHECK("-f", 2, parameterLength)) {
+//            if ((i+1) < argc) {
+//                haveFraction = true;
+//                overlapFraction = atof(argv[i + 1]);
+//                i++;
+//            }
+//        }
+//        else if(PARAMETER_CHECK("-r", 2, parameterLength)) {
+//            reciprocalFraction = true;
+//        }
+//        else if(PARAMETER_CHECK("-valueOnly", 10, parameterLength)) {
+//            valueOnly = true;
+//        }
+//        else {
+//            cerr << endl
+//                 << "*****ERROR: Unrecognized parameter: "
+//                 << argv[i]
+//                 << " *****"
+//                 << endl << endl;
+//            showHelp = true;
+//        }
+//    }
+//
+//    // make sure we have both input files
+//    if (!haveBedA || !haveBedB) {
+//        cerr << endl << "*****" << endl << "*****ERROR: Need -a and -b files. " << endl << "*****" << endl;
+//        showHelp = true;
+//    }
+//
+//    if (reciprocalFraction && !haveFraction) {
+//        cerr << endl << "*****" << endl << "*****ERROR: If using -r, you need to define -f." << endl << "*****" << endl;
+//        showHelp = true;
+//    }
+//
+//    if (!showHelp) {
+//
+//        Jaccard *j = new Jaccard(bedAFile, bedBFile,
+//                                 overlapFraction, reciprocalFraction,
+//                                 valueOnly);
+//        delete j;
+//        return 0;
+//    }
+//    else {
+//        jaccard_help();
+//        return 0;
+//    }
+//}

src/utils/Contexts/ContextJaccard.cpp

+/*
+ * ContextJaccard.cpp
+ *
+ *  Created on: Apr 24, 2014
+ *      Author: nek3d
+ */
+
+#include "ContextJaccard.h"
+
+ContextJaccard::ContextJaccard() {
+	setSortedInput(true);
+	setUseMergedIntervals(true);
+
+}
+
+ContextJaccard::~ContextJaccard() {
+
+}

src/utils/Contexts/ContextJaccard.h

+/*
+ * ContextJaccard.h
+ *
+ *  Created on: Apr 24, 2014
+ *      Author: nek3d
+ */
+
+#ifndef CONTEXTJACCARD_H_
+#define CONTEXTJACCARD_H_