fix blocked_intervals merge conflicts

Makefile

@@ -61,6 +61,7 @@ UTIL_SUBDIRS =	$(SRC_DIR)/utils/lineFileUtilities \
 				$(SRC_DIR)/utils/tabFile \
 				$(SRC_DIR)/utils/BamTools \
 				$(SRC_DIR)/utils/BamTools-Ancillary \
+				$(SRC_DIR)/utils/BlockedIntervals \
 				$(SRC_DIR)/utils/Fasta \
 				$(SRC_DIR)/utils/VectorOps \
 				$(SRC_DIR)/utils/genomeFile

src/annotateBed/Makefile

@@ -15,12 +15,9 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
 # ----------------------------------
 # define our source and object files
 # ----------------------------------
-SOURCES= annotateMain.cpp annotateBed.cpp
-OBJECTS= $(SOURCES:.cpp=.o)
-_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o
-EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
+SOURCES= annotateMain.cpp annotateBed.cpp annotateBed.h
+OBJECTS= annotateMain.o annotateBed.o
 BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
-PROGRAM= annotateBed
 
 
 all: $(BUILT_OBJECTS)
@@ -31,14 +28,9 @@ $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
 	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
 
-$(EXT_OBJECTS):
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/	
 		
 clean:
 	@echo "Cleaning up."
-	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
+	@rm -f $(OBJ_DIR)/annotateMain.o $(OBJ_DIR)/annotateBed.o
 
 .PHONY: clean

src/bamToBed/Makefile

@@ -10,7 +10,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
            -I$(UTILITIES_DIR)/lineFileUtilities/ \
            -I$(UTILITIES_DIR)/fileType/ \
            -I$(UTILITIES_DIR)/BamTools/include \
-		   -I$(UTILITIES_DIR)/BamTools-Ancillary \
+		   -I$(UTILITIES_DIR)/BlockedIntervals \
 		   -I$(UTILITIES_DIR)/version/
 
 
@@ -18,11 +18,8 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
 # define our source and object files
 # ----------------------------------
 SOURCES= bamToBed.cpp
-OBJECTS= $(SOURCES:.cpp=.o)
-_EXT_OBJECTS=BamAncillary.o
-EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
+OBJECTS= bamToBed.o
 BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
-PROGRAM= bamToBed
 
 
 all: $(BUILT_OBJECTS)
@@ -33,11 +30,8 @@ $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
 	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) 
 
-$(EXT_OBJECTS):
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamAncillary/
-	
 clean:
 	@echo "Cleaning up."
-	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
+	@rm -f $(OBJ_DIR)/bamToBed.o
 
 .PHONY: clean

src/bamToBed/bamToBed.cpp

@@ -11,7 +11,7 @@
 ******************************************************************************/
 #include "api/BamReader.h"
 #include "api/BamAux.h"
-#include "BamAncillary.h"
+#include "BlockedIntervals.h"
 #include "bedFile.h"
 #include "version.h"
 using namespace BamTools;
@@ -289,50 +289,10 @@ void ConvertBamToBedpe(const string &bamFile, const bool &useEditDistance) {
 }
 
 
-void ParseCigarBed12(const vector<CigarOp> &cigar, vector<int> &blockStarts, vector<int> &blockLengths, unsigned int &alignmentEnd) {
-
-    int currPosition = 0;
-    int blockLength  = 0;
-
-    //  Rip through the CIGAR ops and figure out if there is more
-    //  than one block for this alignment
-    vector<CigarOp>::const_iterator cigItr = cigar.begin();
-    vector<CigarOp>::const_iterator cigEnd = cigar.end();
-    for (; cigItr != cigEnd; ++cigItr) {
-        switch (cigItr->Type) {
-            case ('M') :
-                blockLength  += cigItr->Length;
-                currPosition += cigItr->Length;
-            case ('I') : break;
-            case ('S') : break;
-            case ('D') : break;
-                blockLength  += cigItr->Length;
-                currPosition += cigItr->Length;
-            case ('P') : break;
-            case ('N') :
-                blockStarts.push_back(currPosition + cigItr->Length);
-                blockLengths.push_back(blockLength);
-                currPosition += cigItr->Length;
-                blockLength = 0;
-            case ('H') : break;                             // for 'H' - do nothing, move to next op
-            default    :
-                printf("ERROR: Invalid Cigar op type\n");   // shouldn't get here
-                exit(1);
-        }
-    }
-    // add the kast block and set the
-    // alignment end (i.e., relative to the start)
-    blockLengths.push_back(blockLength);
-    alignmentEnd = currPosition;
-}
-
-
 string BuildCigarString(const vector<CigarOp> &cigar) {
 
     stringstream cigarString;
-
     for (size_t i = 0; i < cigar.size(); ++i) {
-        //cerr << cigar[i].Type << " " << cigar[i].Length << endl;
         switch (cigar[i].Type) {
             case ('M') :
             case ('I') :
@@ -449,16 +409,18 @@ void PrintBed(const BamAlignment &bam,  const RefVector &refs, bool useEditDista
     // Report each chunk of the BAM alignment as a discrete BED entry
     // For example 10M100N10M would be reported as two seprate BED entries of length 10
     else {
+        // parse the CIGAR string and figure out the alignment blocks
         vector<BED> bedBlocks;
-        // Load the alignment blocks in bam into the bedBlocks vector.
-        // Don't trigger a new block when a "D" (deletion) CIGAR op is found.
-        getBamBlocks(bam, refs, bedBlocks, false);
-
-        vector<BED>::const_iterator bedItr = bedBlocks.begin();
-        vector<BED>::const_iterator bedEnd = bedBlocks.end();
-        for (; bedItr != bedEnd; ++bedItr) {
-            printf("%s\t%d\t%d\t\%s\t%d\t%s\n", refs.at(bam.RefID).RefName.c_str(), bedItr->start,
-                                          bedItr->end, name.c_str(), bam.MapQuality, strand.c_str());
+        string chrom = refs.at(bam.RefID).RefName;
+        // extract the block starts and lengths from the CIGAR string
+        GetBamBlocks(bam, chrom, bedBlocks);
+
+        unsigned int i;
+        for (i = 0; i < bedBlocks.size(); ++i) {
+            BED curr = bedBlocks[i];
+            printf("%s\t%d\t%d\t\%s\t%d\t%s\n", 
+                   chrom.c_str(), curr.start, curr.end,
+                   name.c_str(), bam.MapQuality, strand.c_str());
         }
     }
 }
@@ -476,14 +438,11 @@ void PrintBed12(const BamAlignment &bam, const RefVector &refs, bool useEditDist
     if (bam.IsSecondMate()) name += "/2";
 
     // parse the CIGAR string and figure out the alignment blocks
-    unsigned int alignmentEnd;
-    vector<int> blockLengths;
-    vector<int> blockStarts;
-    blockStarts.push_back(0);
-
+    vector<BED> bedBlocks;
+    string chrom = refs.at(bam.RefID).RefName;
+    CHRPOS alignmentEnd = bam.GetEndPosition();
     // extract the block starts and lengths from the CIGAR string
-    ParseCigarBed12(bam.CigarData, blockStarts, blockLengths, alignmentEnd);
-    alignmentEnd += bam.Position;
+    GetBamBlocks(bam, chrom, bedBlocks);
 
     // write BED6 portion
     if (useEditDistance == false && bamTag == "") {
@@ -514,20 +473,20 @@ void PrintBed12(const BamAlignment &bam, const RefVector &refs, bool useEditDist
     }
 
     // write the colors, etc.
-    printf("%d\t%d\t%s\t%d\t", bam.Position, alignmentEnd, color.c_str(), (int) blockStarts.size());
+    printf("%d\t%d\t%s\t%d\t", bam.Position, alignmentEnd, color.c_str(), (int) bedBlocks.size());
 
     // now write the lengths portion
     unsigned int b;
-    for (b = 0; b < blockLengths.size() - 1; ++b) {
-        printf("%d,", blockLengths[b]);
+    for (b = 0; b < bedBlocks.size() - 1; ++b) {
+        printf("%d,", bedBlocks[b].end - bedBlocks[b].start);
     }
-    printf("%d\t", blockLengths[b]);
+    printf("%d\t", bedBlocks[b].end - bedBlocks[b].start);
 
     // now write the starts portion
-    for (b = 0; b < blockStarts.size() - 1; ++b) {
-        printf("%d,", blockStarts[b]);
+    for (b = 0; b < bedBlocks.size() - 1; ++b) {
+        printf("%d,", bedBlocks[b].start - bam.Position);
     }
-    printf("%d\n", blockStarts[b]);
+    printf("%d\n", bedBlocks[b].start - bam.Position);
 }
 
 

src/bed12ToBed6/Makefile

@@ -9,17 +9,16 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
            -I$(UTILITIES_DIR)/lineFileUtilities/ \
            -I$(UTILITIES_DIR)/gzstream/ \
            -I$(UTILITIES_DIR)/fileType/ \
+           -I$(UTILITIES_DIR)/BamTools/include \
+		   -I$(UTILITIES_DIR)/BlockedIntervals \
            -I$(UTILITIES_DIR)/version/
 
 # ----------------------------------
 # define our source and object files
 # ----------------------------------
 SOURCES= bed12ToBed6.cpp
-OBJECTS= $(SOURCES:.cpp=.o)
-_EXT_OBJECTS=bedFile.o  lineFileUtilities.o gzstream.o fileType.o
-EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
+OBJECTS= bed12ToBed6.o
 BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
-PROGRAM= bed12ToBed6
 
 
 all: $(BUILT_OBJECTS)
@@ -30,14 +29,8 @@ $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
 	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
 
-$(EXT_OBJECTS):	
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/
-			
 clean:
 	@echo "Cleaning up."
-	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
+	@rm -f $(OBJ_DIR)/bed12ToBed6.o
 
 .PHONY: clean

src/bed12ToBed6/bed12ToBed6.cpp

@@ -10,6 +10,7 @@
   Licenced under the GNU General Public License 2.0 license.
 ******************************************************************************/
 #include "lineFileUtilities.h"
+#include "BlockedIntervals.h"
 #include "bedFile.h"
 #include "version.h"
 #include <vector>
@@ -140,7 +141,7 @@ void ProcessBed(istream &bedInput, BedFile *bed) {
         if (bed->_status == BED_VALID) {
 
             bedVector bedBlocks;  // vec to store the discrete BED "blocks" from a
-            splitBedIntoBlocks(bedEntry, bedBlocks);
+            GetBedBlocks(bedEntry, bedBlocks);
 
             for (int i = 0; i < (int) bedBlocks.size(); ++i) {
                 if (addBlockNums == false) {

src/bedToBam/Makefile

@@ -19,9 +19,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
 # define our source and object files
 # ----------------------------------
 SOURCES= bedToBam.cpp
-OBJECTS= $(SOURCES:.cpp=.o)
-_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o fileType.o
-EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
+OBJECTS= bedToBam.o
 BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
 PROGRAM= bedToBam
 
@@ -34,16 +32,8 @@ $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
 	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
 
-$(EXT_OBJECTS):
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/	
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/genomeFile/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/
-				
 clean:
 	@echo "Cleaning up."
-	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
+	@rm -f $(OBJ_DIR)/bedToBam.o
 
 .PHONY: clean

src/bedToIgv/Makefile

@@ -17,9 +17,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
 # define our source and object files
 # ----------------------------------
 SOURCES= bedToIgv.cpp
-OBJECTS= $(SOURCES:.cpp=.o)
-_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o fileType.o
-EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
+OBJECTS= bedToIgv.o
 BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
 PROGRAM= bedToIgv
 
@@ -32,15 +30,8 @@ $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
 	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
 
-$(EXT_OBJECTS):
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/genomeFile/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/
-				
 clean:
 	@echo "Cleaning up."
-	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
+	@rm -f $(OBJ_DIR)/bedToIgv.o
 
 .PHONY: clean

src/closestBed/Makefile

@@ -13,12 +13,9 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
 # ----------------------------------
 # define our source and object files
 # ----------------------------------
-SOURCES= closestMain.cpp closestBed.cpp
-OBJECTS= $(SOURCES:.cpp=.o)
-_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o
-EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
+SOURCES= closestMain.cpp closestBed.cpp closestBed.h
+OBJECTS= closestMain.o closestBed.o
 BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
-PROGRAM= closestBed
 
 all: $(BUILT_OBJECTS)
 
@@ -28,14 +25,8 @@ $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
 	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
 
-$(EXT_OBJECTS):
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/	
-
 clean:
 	@echo "Cleaning up."
-	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
-
+	@rm -f $(OBJ_DIR)/closestMain.o  $(OBJ_DIR)/closestBed.o
+	
 .PHONY: clean

src/clusterBed/Makefile

@@ -14,10 +14,8 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
 # ----------------------------------
 # define our source and object files
 # ----------------------------------
-SOURCES= clusterMain.cpp clusterBed.cpp
-OBJECTS= $(SOURCES:.cpp=.o)
-_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o
-EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
+SOURCES= clusterMain.cpp clusterBed.cpp clusterBed.h
+OBJECTS= clusterMain.o clusterBed.o
 BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
 
 
@@ -29,15 +27,8 @@ $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
 	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
 
-$(EXT_OBJECTS):
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/
-			
 clean:
 	@echo "Cleaning up."
-	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
+	@rm -f $(OBJ_DIR)/clusterMain.o $(OBJ_DIR)/clusterBed.o
 
 .PHONY: clean
\ No newline at end of file

src/complementBed/Makefile

@@ -16,10 +16,8 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
 # ----------------------------------
 # define our source and object files
 # ----------------------------------
-SOURCES= complementMain.cpp complementBed.cpp
-OBJECTS= $(SOURCES:.cpp=.o)
-_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o fileType.o
-EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
+SOURCES= complementMain.cpp complementBed.cpp complementBed.h
+OBJECTS= complementMain.o complementBed.o
 BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
 PROGRAM= complementBed
 
@@ -32,15 +30,9 @@ $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
 	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
 
-$(EXT_OBJECTS):
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/	
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/genomeFile/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/
-	
+
 clean:
 	@echo "Cleaning up."
-	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
+	@rm -f $(OBJ_DIR)/complementMain.o $(OBJ_DIR)/complementBed.o
 
 .PHONY: clean

src/coverageBed/Makefile

@@ -11,18 +11,14 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
            -I$(UTILITIES_DIR)/lineFileUtilities/ \
            -I$(UTILITIES_DIR)/fileType/ \
            -I$(UTILITIES_DIR)/BamTools/include \
-		   -I$(UTILITIES_DIR)/BamTools-Ancillary \
+		   -I$(UTILITIES_DIR)/BlockedIntervals \
 		   -I$(UTILITIES_DIR)/version/
 # ----------------------------------
 # define our source and object files
 # ----------------------------------
-SOURCES= coverageMain.cpp coverageBed.cpp
-OBJECTS= $(SOURCES:.cpp=.o)
-_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o BamAncillary.o
-EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
+SOURCES= coverageMain.cpp coverageBed.cpp coverageBed.h
+OBJECTS= coverageMain.o coverageBed.o
 BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
-PROGRAM= coverageBed
-
 
 all: $(BUILT_OBJECTS)
 
@@ -32,16 +28,8 @@ $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
 	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
 
-$(EXT_OBJECTS):
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/	
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools-Ancillary/	
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/	
-		
 clean:
 	@echo "Cleaning up."
-	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
+	@rm -f $(OBJ_DIR)/coverageMain.o $(OBJ_DIR)/coverageBed.o 
 
 .PHONY: clean

src/coverageBed/coverageBed.cpp

@@ -62,7 +62,7 @@ void BedCoverage::CollectCoverageBed() {
             // split the BED into discrete blocksand process each independently.
             else {
                 bedVector bedBlocks;
-                splitBedIntoBlocks(a, bedBlocks);
+                GetBedBlocks(a, bedBlocks);
                 // use countSplitHits to avoid over-counting each split chunk
                 // as distinct read coverage.
                 _bedB->countSplitHits(bedBlocks, _sameStrand, _diffStrand, _countsOnly);
@@ -117,7 +117,7 @@ void BedCoverage::CollectCoverageBam(string bamFile) {
                 bedVector bedBlocks;
                 // since we are counting coverage, we do want to split blocks when a
                 // deletion (D) CIGAR op is encountered (hence the true for the last parm)
-                getBamBlocks(bam, refs, bedBlocks, true);
+                GetBamBlocks(bam, refs.at(bam.RefID).RefName, bedBlocks, true);
                 // use countSplitHits to avoid over-counting each split chunk
                 // as distinct read coverage.
                 _bedB->countSplitHits(bedBlocks, _sameStrand, _diffStrand, _countsOnly);

src/coverageBed/coverageBed.h

@@ -16,7 +16,7 @@
 
 #include "api/BamReader.h"
 #include "api/BamAux.h"
-#include "BamAncillary.h"
+#include "BlockedIntervals.h"
 using namespace BamTools;
 
 #include <vector>

src/fastaFromBed/Makefile

@@ -17,12 +17,9 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
 # ----------------------------------
 # define our source and object files
 # ----------------------------------
-SOURCES= fastaFromBedMain.cpp fastaFromBed.cpp
-OBJECTS= $(SOURCES:.cpp=.o)
-_EXT_OBJECTS=bedFile.o sequenceUtils.o lineFileUtilities.o gzstream.o fileType.o Fasta.o split.o
-EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
+SOURCES= fastaFromBedMain.cpp fastaFromBed.cpp fastaFromBed.h
+OBJECTS= fastaFromBedMain.o fastaFromBed.o
 BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
-PROGRAM= fastaFromBed
 
 
 all: $(BUILT_OBJECTS)
@@ -33,16 +30,8 @@ $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
 	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
 
-$(EXT_OBJECTS):
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/sequenceUtilities/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/Fasta/
-		
 clean:
 	@echo "Cleaning up."
-	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
+	@rm -f $(OBJ_DIR)/fastaFromBedMain.o $(OBJ_DIR)/fastaFromBed.o
 
 .PHONY: clean
\ No newline at end of file

src/flankBed/Makefile

@@ -16,13 +16,9 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
 # ----------------------------------
 # define our source and object files
 # ----------------------------------
-SOURCES= flankBedMain.cpp flankBed.cpp
-OBJECTS= $(SOURCES:.cpp=.o)
-_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o fileType.o
-EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
+SOURCES= flankBedMain.cpp flankBed.cpp flankBed.h
+OBJECTS= flankBedMain.o flankBed.o
 BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
-PROGRAM= flankBed
-
 
 all: $(BUILT_OBJECTS)
 
@@ -31,16 +27,9 @@ all: $(BUILT_OBJECTS)
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
 	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
-
-$(EXT_OBJECTS):
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/genomeFile/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/	
 		
 clean:
 	@echo "Cleaning up."
-	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
-
+	@rm -f $(OBJ_DIR)/flankBedMain.o $(OBJ_DIR)/flankBed.o
+	
 .PHONY: clean

src/genomeCoverageBed/Makefile

@@ -11,17 +11,14 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
            -I$(UTILITIES_DIR)/lineFileUtilities/ \
            -I$(UTILITIES_DIR)/fileType/ \
            -I$(UTILITIES_DIR)/BamTools/include \
-		   -I$(UTILITIES_DIR)/BamTools-Ancillary \
+		   -I$(UTILITIES_DIR)/BlockedIntervals \
 		   -I$(UTILITIES_DIR)/version/
 # ----------------------------------
 # define our source and object files
 # ----------------------------------
-SOURCES= genomeCoverageMain.cpp genomeCoverageBed.cpp
-OBJECTS= $(SOURCES:.cpp=.o)
-_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o BamAncillary.o gzstream.o fileType.o
-EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
+SOURCES= genomeCoverageMain.cpp genomeCoverageBed.cpp genomeCoverageBed.h
+OBJECTS= genomeCoverageMain.o genomeCoverageBed.o
 BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
-PROGRAM= genomeCoverageBed
 
 
 all: $(BUILT_OBJECTS)
@@ -32,17 +29,8 @@ $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
 	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
 
-$(EXT_OBJECTS):
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/genomeFile
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools-Ancillary/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/	
-		
 clean:
 	@echo "Cleaning up."
-	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
+	@rm -f $(OBJ_DIR)/genomeCoverageMain.o $(OBJ_DIR)/genomeCoverageBed.o
 
 .PHONY: clean

src/genomeCoverageBed/genomeCoverageBed.cpp

@@ -172,7 +172,7 @@ void BedGenomeCoverage::CoverageBed() {
 
             if (_obeySplits == true) {
                 bedVector bedBlocks; // vec to store the discrete BED "blocks"
-                splitBedIntoBlocks(a, bedBlocks);
+                GetBedBlocks(a, bedBlocks);
                 AddBlockedCoverage(bedBlocks);
             }
             else if (_only_5p_end) {
@@ -247,7 +247,7 @@ void BedGenomeCoverage::CoverageBam(string bamFile) {
             bedVector bedBlocks;
             // since we are counting coverage, we do want to split blocks when a
             // deletion (D) CIGAR op is encountered (hence the true for the last parm)
-            getBamBlocks(bam, refs, bedBlocks, true);
+            GetBamBlocks(bam, refs.at(bam.RefID).RefName, bedBlocks, true);
             AddBlockedCoverage(bedBlocks);
         }
         else if (_only_5p_end) {

src/genomeCoverageBed/genomeCoverageBed.h

@@ -12,7 +12,7 @@ Licenced under the GNU General Public License 2.0 license.
 #include "bedFile.h"
 #include "genomeFile.h"
 
-#include "BamAncillary.h"
+#include "BlockedIntervals.h"
 #include "api/BamReader.h"
 #include "api/BamAux.h"
 using namespace BamTools;

src/getOverlap/Makefile

@@ -16,11 +16,8 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
 # define our source and object files
 # ----------------------------------
 SOURCES= getOverlap.cpp
-OBJECTS= $(SOURCES:.cpp=.o)
-_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o
-EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
+OBJECTS= getOverlap.o
 BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
-PROGRAM= getOverlap
 
 
 all: $(BUILT_OBJECTS)
@@ -31,16 +28,9 @@ $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
 	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
 
-$(EXT_OBJECTS):
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/	
-	
-
 	
 clean:
 	@echo "Cleaning up."
-	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
+	@rm -f $(OBJ_DIR)/getOverlap.o
 
 .PHONY: clean