added new "spacing" tool to report distances between intervals in a single file.

Makefile

@@ -53,7 +53,7 @@ SUBDIRS = $(SRC_DIR)/annotateBed \
 		  $(SRC_DIR)/mergeFile \
 		  $(SRC_DIR)/multiBamCov \
 		  $(SRC_DIR)/multiIntersectBed \
-		   $(SRC_DIR)/nekSandbox1 \
+		  $(SRC_DIR)/nekSandbox1 \
 		  $(SRC_DIR)/nucBed \
 		  $(SRC_DIR)/pairToBed \
 		  $(SRC_DIR)/pairToPair \
@@ -64,6 +64,7 @@ SUBDIRS = $(SRC_DIR)/annotateBed \
 		  $(SRC_DIR)/shuffleBed \
 		  $(SRC_DIR)/slopBed \
 		  $(SRC_DIR)/sortBed \
+		  $(SRC_DIR)/spacingFile \
 		  $(SRC_DIR)/split \
 		  $(SRC_DIR)/subtractBed \
 		  $(SRC_DIR)/tagBam \

src/bedtools.cpp

@@ -72,6 +72,7 @@ int shuffle_main(int argc, char* argv[]); //
 int slop_main(int argc, char* argv[]); //
 int split_main(int argc, char* argv[]); //
 int sort_main(int argc, char* argv[]); //
+int spacing_main(int argc, char* argv[]); //
 int subtract_main(int argc, char* argv[]); //
 int tagbam_main(int argc, char* argv[]);//
 int unionbedgraphs_main(int argc, char* argv[]);//
@@ -105,6 +106,7 @@ int main(int argc, char *argv[])
     else if (sub_cmd == "sort")        return sort_main(argc-1, argv+1);
     else if (sub_cmd == "random")      return random_main(argc-1, argv+1);
     else if (sub_cmd == "shuffle")     return shuffle_main(argc-1, argv+1);
+    else if (sub_cmd == "spacing")     return spacing_main(argc-1, argv+1);
     else if (sub_cmd == "annotate")    return annotate_main(argc-1, argv+1);
 
     // Multi-way file comparisonstools
@@ -207,7 +209,8 @@ int bedtools_help(void)
     cout  << "    sort          "  << "Order the intervals in a file.\n";
     cout  << "    random        "  << "Generate random intervals in a genome.\n";
     cout  << "    shuffle       "  << "Randomly redistrubute intervals in a genome.\n";
-    cout  << "    sample        "  << "Sample random records from file using reservoir sampling.\n";    
+    cout  << "    sample        "  << "Sample random records from file using reservoir sampling.\n";   
+    cout  << "    spacing       "  << "Report the spacing between intervals in a file.\n";     
     cout  << "    annotate      "  << "Annotate coverage of features from multiple files.\n";
     
     cout  << endl;
@@ -253,6 +256,7 @@ int bedtools_help(void)
     cout  << "    makewindows   "  << "Make interval \"windows\" across a genome.\n";
     cout  << "    groupby       "  << "Group by common cols. & summarize oth. cols. (~ SQL \"groupBy\")\n";
     cout  << "    expand        "  << "Replicate lines based on lists of values in columns.\n";
+    cout  << "    split         "  << "Split a file into multiple files with equal records or base pairs.\n"; 
 
     cout  << endl;
     cout  << "[ General help ]" << endl;

src/utils/Contexts/ContextBase.cpp

@@ -64,6 +64,7 @@ ContextBase::ContextBase()
 {
 	_programNames["intersect"] = INTERSECT;
 	_programNames["sample"] = SAMPLE;
+	_programNames["spacing"] = SPACING;
 	_programNames["map"] = MAP;
 	_programNames["merge"] = MERGE;
 

src/utils/Contexts/ContextBase.h

@@ -38,7 +38,7 @@ public:
 	typedef enum {UNSPECIFIED_PROGRAM, INTERSECT, WINDOW, CLOSEST, COVERAGE, MAP, GENOMECOV, MERGE, CLUSTER,
 		COMPLEMENT, SUBTRACT, SLOP, FLANK, SORT, RANDOM, SAMPLE, SHUFFLE, ANNOTATE, MULTIINTER, UNIONBEDG, PAIRTOBED,
 		PAIRTOPAIR,BAMTOBED, BEDTOBAM, BEDTOFASTQ, BEDPETOBAM, BED12TOBED6, GETFASTA, MASKFASTA, NUC,
-		MULTICOV, TAG, JACCARD, OVERLAP, IGV, LINKS,MAKEWINDOWS, GROUPBY, EXPAND } PROGRAM_TYPE;
+		MULTICOV, TAG, JACCARD, OVERLAP, IGV, LINKS,MAKEWINDOWS, GROUPBY, EXPAND, SPACING } PROGRAM_TYPE;
 
 	PROGRAM_TYPE getProgram() const { return _program; }
 	FileRecordMgr *getFile(int fileIdx) { return _files[fileIdx]; }

src/utils/Contexts/Makefile

@@ -20,9 +20,9 @@ INCLUDES =  -I$(UTILITIES_DIR)/general/ \
 # define our source and object files
 # ----------------------------------
 SOURCES= ContextBase.cpp ContextBase.h ContextIntersect.cpp ContextIntersect.h ContextFisher.cpp ContextFisher.h ContextMap.cpp \
-	ContextMap.h ContextSample.cpp ContextSample.h ContextMerge.h ContextMerge.cpp ContextJaccard.h ContextJaccard.cpp \
+	ContextMap.h ContextSample.cpp ContextSpacing.cpp ContextSample.h ContextSpacing.h ContextMerge.h ContextMerge.cpp ContextJaccard.h ContextJaccard.cpp \
 	ContextClosest.cpp ContextClosest.h
-OBJECTS= ContextBase.o ContextIntersect.o ContextFisher.o ContextMap.o ContextSample.o ContextMerge.o ContextJaccard.o ContextClosest.o
+OBJECTS= ContextBase.o ContextIntersect.o ContextFisher.o ContextMap.o ContextSample.o ContextSpacing.o ContextMerge.o ContextJaccard.o ContextClosest.o
 _EXT_OBJECTS=ParseTools.o QuickString.o
 EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
 BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
@@ -42,6 +42,7 @@ clean:
 	       $(OBJ_DIR)/ContextFisher.o \
 	       $(OBJ_DIR)/ContextMap.o \
 	       $(OBJ_DIR)/ContextSample.o \
+	       $(OBJ_DIR)/ContextSpacing.o \
 	       $(OBJ_DIR)/ContextMerge.o \
 	       $(OBJ_DIR)/ContextJaccard.o \
 	       $(OBJ_DIR)/ContextClosest.o \

src/utils/RecordOutputMgr/RecordOutputMgr.cpp

@@ -273,6 +273,10 @@ void RecordOutputMgr::printRecord(RecordKeyVector &keyList, RecordKeyVector *blo
 		printKeyAndTerminate(keyList);
 		_currBamBlockList = NULL;
 
+		return;
+	} else if (_context->getProgram() == ContextBase::SPACING) {
+		keyList.getKey()->print(_outBuf);
+		_currBamBlockList = NULL;
 		return;
 	}
 }