initial go at -exclude for fisher

src/fisher/Fisher.cpp

@@ -12,6 +12,14 @@ Fisher::Fisher(ContextFisher *context)
   _dbLen(0)
 {
     _blockMgr = new BlockMgr(_context->getOverlapFraction(), _context->getReciprocal());
+    _haveExclude = false;
+
+    if(!(_context->getExcludeFile().empty())){
+        string ex = _context->getExcludeFile();
+        exclude = new BedFile(ex);
+        exclude->loadBedFileIntoMergedMap();
+        _haveExclude = true;
+    }
 }
 
 Fisher::~Fisher(void) {
@@ -36,6 +44,9 @@ bool Fisher::calculate() {
     double left, right, two;
 
     long long genomeSize = _context->getGenomeFile()->getGenomeSize();
+    if(_haveExclude){
+        genomeSize -= exclude->getTotalFlattenedLength();
+    }
     // bases covered by neither a nor b
     long long n11 = genomeSize - _queryLen - _dbLen + _intersectionVal;
     // bases covered only by -b
@@ -46,9 +57,9 @@ bool Fisher::calculate() {
     long long n22 = _intersectionVal;
 
     printf("#_________________________________________\n");
-    printf("#        | %-12s | %-12s |\n", "not in -b", "in -b");
+    printf("#           | %-12s | %-12s |\n", "not in -b", "in -b");
     printf("# not in -a | %-12lld | %-12lld |\n", n11, n12);
-    printf("#      in -a | %-12lld | %-12lld |\n", n21, n22);
+    printf("#     in -a | %-12lld | %-12lld |\n", n21, n22);
     printf("#_________________________________________\n");
 
     kt_fisher_exact(n11, n12, n21, n22, &left, &right, &two);
@@ -66,6 +77,7 @@ bool Fisher::getFisher() {
     if (!sweep.init()) {
         return false;
     }
+
     RecordKeyVector hitSet;
     while (sweep.next(hitSet)) {
         if (_context->getObeySplits()) {

src/fisher/Fisher.h

 #ifndef FISHER_H
 #define FISHER_H
 
+#include "bedFile.h"
+#include "bedFilePE.h"
+
 #include "ContextFisher.h"
 
 class BlockMgr;
@@ -19,10 +22,12 @@ private:
     BlockMgr *_blockMgr;
     unsigned long _intersectionVal;
     unsigned long _unionVal;
+    bool _haveExclude;
     int _numIntersections;
     unsigned long _queryLen;
     unsigned long _dbLen;
     bool getFisher();
+    BedFile *exclude;
 
     unsigned long getTotalIntersection(RecordKeyVector &hits);
 };

src/fisher/Makefile

@@ -9,27 +9,32 @@ BIN_DIR = ../../bin/
 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)/FileRecordTools/ \
-           -I$(UTILITIES_DIR)/FileRecordTools/FileReaders/ \
-           -I$(UTILITIES_DIR)/FileRecordTools/Records/ \
-           -I$(UTILITIES_DIR)/RecordOutputMgr/ \
+		    -I$(UTILITIES_DIR)/gzstream/ \
+		   -I$(UTILITIES_DIR)/bedFile/ \
+		   -I$(UTILITIES_DIR)/bedFilePE/ \
+		   -I$(UTILITIES_DIR)/GenomeFile/ \
+		   -I$(UTILITIES_DIR)/lineFileUtilities/ \
+		           -I$(UTILITIES_DIR)/BamTools/include \
+		           -I$(UTILITIES_DIR)/BamTools/src \
+		           -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)/RecordOutputMgr/ \
 			-I$(UTILITIES_DIR)/KeyListOps/ \
-           -I$(UTILITIES_DIR)/NewChromsweep \
-           -I$(UTILITIES_DIR)/VectorOps \
+		           -I$(UTILITIES_DIR)/NewChromsweep \
+		           -I$(UTILITIES_DIR)/VectorOps \
 		   -I . \
-           -I$(UTILITIES_DIR)/BinTree \
-           -I$(UTILITIES_DIR)/version/
+		           -I$(UTILITIES_DIR)/BinTree \
+		           -I$(UTILITIES_DIR)/version/
 
 # ----------------------------------
 # define our source and object files
 # ----------------------------------
-SOURCES= fisherMain.cpp Fisher.cpp Fisher.h kfunc.c
+SOURCES= fisherMain.cpp Fisher.cpp Fisher.h kfunc.c \
+		 ../utils/Contexts/ContextFisher.cpp \
+		 ../utils/Contexts/ContextFisher.h
 OBJECTS= fisherMain.o Fisher.o
 BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
 PROGRAM= Fisher

src/utils/Contexts/ContextFisher.cpp

@@ -8,7 +8,6 @@
 ContextFisher::ContextFisher() {
 	setSortedInput(true);
 	setUseMergedIntervals(true);
-
 }
 
 ContextFisher::~ContextFisher() {
@@ -38,6 +37,9 @@ bool ContextFisher::parseCmdArgs(int argc, char **argv, int skipFirstArgs)
 		else if (strcmp(_argv[_i], "-S") == 0) {
 			if (!handle_S()) return false;
 		}
+		else if (strcmp(_argv[_i], "-exclude") == 0) {
+			if (!handle_exclude()) return false;
+		}
         if (strcmp(_argv[_i], "-g") == 0) {
               if (!handle_g()) return false;
         }
@@ -112,4 +114,19 @@ bool ContextFisher::handle_S() {
 	return false;
 }
 
+bool ContextFisher::handle_exclude()
+{
+    if (_argc <= _i+1) {
+        _errorMsg = "\n***** ERROR: -exclude option given, but no file specified. *****";
+        return false;
+    }
+
+    do {
+        markUsed(_i - _skipFirstArgs);
+        _i++;
+        markUsed(_i - _skipFirstArgs);
+    } while (_argc > _i+1 && _argv[_i+1][0] != '-');
+    setExcludeFile(string(_argv[_i]));
+    return true;
+}
 

src/utils/Contexts/ContextFisher.h

@@ -17,10 +17,17 @@ public:
   ~ContextFisher();
 	virtual bool parseCmdArgs(int argc, char **argv, int skipFirstArgs);
 	virtual bool isValidState();
+	string getExcludeFile() { return _excludeFile; }
+	void setExcludeFile(string excludeFile) { _excludeFile = excludeFile; }
+
 
 private:
 	bool handle_s();
 	bool handle_S();
+	bool handle_exclude();
+	string _excludeFile;
+
+
 };
 
 #endif /* CONTEXTFISHER_H_ */

src/utils/bedFile/bedFile.cpp

@@ -657,12 +657,24 @@ void BedFile::setBed12 (bool isBed12) { this->isBed12 = isBed12; }
 void BedFile::loadBedFileIntoMap() {
 
     BED bedEntry;
-    
+
     Open();
     while (GetNextBed(bedEntry)) {
         if (_status == BED_VALID) {
-            BIN bin = getBin(bedEntry.start, bedEntry.end);
-            bedMap[bedEntry.chrom][bin].push_back(bedEntry);
+            addBEDIntoMap(bedEntry);
+        }
+    }
+    Close();
+}
+
+void BedFile::loadBedFileIntoMergedMap() {
+
+    BED bedEntry;
+
+    Open();
+    while (GetNextMergedBed(bedEntry)) {
+        if (_status == BED_VALID) {
+            addBEDIntoMap(bedEntry);
         }
     }
     Close();

src/utils/bedFile/bedFile.h

@@ -418,6 +418,7 @@ public:
     // load a BED file into a map keyed by chrom, then bin. value is 
     // vector of BEDs
     void loadBedFileIntoMap();
+    void loadBedFileIntoMergedMap();
 
     // load a BED entry into and existing map
     void addBEDIntoMap(BED bedEntry);