First commit for new 2.18-alpha branch.

Makefile

@@ -16,11 +16,11 @@ export BIN_DIR	= bin
 export SRC_DIR	= src
 export UTIL_DIR	= src/utils
 export CXX		= g++
-ifeq ($(DEBUG),1)
-export CXXFLAGS = -Wall -O0 -g -fno-inline -fkeep-inline-functions -D_FILE_OFFSET_BITS=64 -fPIC -DDEBUG -D_DEBUG
-else
+#ifeq ($(DEBUG),1)
+#export CXXFLAGS = -Wall -O0 -g -fno-inline -fkeep-inline-functions -D_FILE_OFFSET_BITS=64 -fPIC -DDEBUG -D_DEBUG
+#else
 export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC
-endif
+#endif
 export LIBS		= -lz
 export BT_ROOT  = src/utils/BamTools/
 
@@ -42,18 +42,20 @@ SUBDIRS = $(SRC_DIR)/annotateBed \
 		  $(SRC_DIR)/genomeCoverageBed \
 		  $(SRC_DIR)/getOverlap \
 		  $(SRC_DIR)/groupBy \
-		  $(SRC_DIR)/intersectBed \
+		  $(SRC_DIR)/intersectFile \
 		  $(SRC_DIR)/jaccard \
 		  $(SRC_DIR)/linksBed \
 		  $(SRC_DIR)/maskFastaFromBed \
 		  $(SRC_DIR)/mapBed \
 		  $(SRC_DIR)/mergeBed \
 		  $(SRC_DIR)/multiBamCov \
 		  $(SRC_DIR)/multiIntersectBed \
+		   $(SRC_DIR)/nekSandbox1 \
 		  $(SRC_DIR)/nucBed \
 		  $(SRC_DIR)/pairToBed \
 		  $(SRC_DIR)/pairToPair \
 		  $(SRC_DIR)/randomBed \
+		  $(SRC_DIR)/regressTest \
 		  $(SRC_DIR)/reldist \
 		  $(SRC_DIR)/shuffleBed \
 		  $(SRC_DIR)/slopBed \
@@ -65,20 +67,25 @@ SUBDIRS = $(SRC_DIR)/annotateBed \
 		  $(SRC_DIR)/windowMaker
 
 UTIL_SUBDIRS =	$(SRC_DIR)/utils/bedFile \
+				$(SRC_DIR)/utils/BinTree \
 				$(SRC_DIR)/utils/version \
 				$(SRC_DIR)/utils/bedGraphFile \
 				$(SRC_DIR)/utils/chromsweep \
+				$(SRC_DIR)/utils/Contexts \
+				$(SRC_DIR)/utils/FileRecordTools \
+				$(SRC_DIR)/utils/general \
 				$(SRC_DIR)/utils/gzstream \
 				$(SRC_DIR)/utils/fileType \
 				$(SRC_DIR)/utils/bedFilePE \
+				$(SRC_DIR)/utils/NewChromsweep \
 				$(SRC_DIR)/utils/sequenceUtilities \
 				$(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_DIR)/utils/GenomeFile
 
 BUILT_OBJECTS = $(OBJ_DIR)/*.o
 

src/bedToBam/Makefile

@@ -8,7 +8,7 @@ BIN_DIR = ../../bin/
 INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
            -I$(UTILITIES_DIR)/version/ \
            -I$(UTILITIES_DIR)/gzstream/ \
-           -I$(UTILITIES_DIR)/genomeFile/ \
+           -I$(UTILITIES_DIR)/GenomeFile/ \
            -I$(UTILITIES_DIR)/lineFileUtilities/ \
            -I$(UTILITIES_DIR)/fileType/ \
            -I$(UTILITIES_DIR)/BamTools/include \

src/bedToBam/bedToBam.cpp

@@ -11,7 +11,7 @@
 ******************************************************************************/
 #include "lineFileUtilities.h"
 #include "bedFile.h"
-#include "genomeFile.h"
+#include "GenomeFile.h"
 #include "version.h"
 
 

src/bedToIgv/Makefile

@@ -6,7 +6,7 @@ BIN_DIR = ../../bin/
 # define our includes
 # -------------------
 INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
-           -I$(UTILITIES_DIR)/genomeFile/ \
+           -I$(UTILITIES_DIR)/GenomeFile/ \
            -I$(UTILITIES_DIR)/lineFileUtilities/ \
            -I$(UTILITIES_DIR)/gzstream/ \
            -I$(UTILITIES_DIR)/fileType/ \

src/bedToIgv/bedToIgv.cpp

@@ -11,7 +11,7 @@
 ******************************************************************************/
 #include "lineFileUtilities.h"
 #include "bedFile.h"
-#include "genomeFile.h"
+#include "GenomeFile.h"
 #include "version.h"
 
 #include <vector>

src/bedpeToBam/Makefile

@@ -9,7 +9,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
            -I$(UTILITIES_DIR)/bedFilePE/ \
            -I$(UTILITIES_DIR)/version/ \
            -I$(UTILITIES_DIR)/gzstream/ \
-           -I$(UTILITIES_DIR)/genomeFile/ \
+           -I$(UTILITIES_DIR)/GenomeFile/ \
            -I$(UTILITIES_DIR)/lineFileUtilities/ \
            -I$(UTILITIES_DIR)/fileType/ \
            -I$(UTILITIES_DIR)/BamTools/include \

src/bedpeToBam/bedpeToBam.cpp

@@ -11,7 +11,7 @@
 ******************************************************************************/
 #include "lineFileUtilities.h"
 #include "bedFilePE.h"
-#include "genomeFile.h"
+#include "GenomeFile.h"
 #include "version.h"
 
 

src/bedtools.cpp

@@ -45,6 +45,7 @@ int closest_main(int argc, char* argv[]); //
 int cluster_main(int argc, char* argv[]); //
 int complement_main(int argc, char* argv[]);//
 int coverage_main(int argc, char* argv[]); //
+int regress_test_main(int argc, char **argv); //
 int expand_main(int argc, char* argv[]);//
 int fastafrombed_main(int argc, char* argv[]);//
 int flank_main(int argc, char* argv[]); //
@@ -59,6 +60,7 @@ int map_main(int argc, char* argv[]); //
 int merge_main(int argc, char* argv[]); //
 int multibamcov_main(int argc, char* argv[]);//
 int multiintersect_main(int argc, char* argv[]);//
+int nek_sandbox1_main(int argc, char* argv[]);//
 int nuc_main(int argc, char* argv[]);//
 int pairtobed_main(int argc, char* argv[]);//
 int pairtopair_main(int argc, char* argv[]);//
@@ -136,9 +138,8 @@ int main(int argc, char *argv[])
     else if (sub_cmd == "makewindows") return windowmaker_main(argc-1, argv+1);
     else if (sub_cmd == "groupby")     return groupby_main(argc-1, argv+1);
     else if (sub_cmd == "expand")      return expand_main(argc-1, argv+1);
-
-
-
+    else if (sub_cmd == "neksb1")	   	return nek_sandbox1_main(argc-1, argv+1);
+    else if (sub_cmd == "regresstest")	return regress_test_main(argc, argv); //this command does need all the orig args.
     // help
     else if (sub_cmd == "-h" || sub_cmd == "--help" ||
              sub_cmd == "-help")
@@ -230,7 +231,7 @@ int bedtools_help(void)
     cout  << "[ BAM focused tools ]" << endl;
     cout  << "    multicov      "  << "Counts coverage from multiple BAMs at specific intervals.\n";
     cout  << "    tag           "  << "Tag BAM alignments based on overlaps with interval files.\n";
-    
+
     cout  << endl;
     cout  << "[ Statistical relationships ]" << endl;
     cout  << "    jaccard       "  << "Calculate the Jaccard statistic b/w two sets of intervals.\n";

src/complementBed/Makefile

@@ -6,7 +6,7 @@ BIN_DIR = ../../bin/
 # define our includes
 # -------------------
 INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
-           -I$(UTILITIES_DIR)/genomeFile/ \
+           -I$(UTILITIES_DIR)/GenomeFile/ \
            -I$(UTILITIES_DIR)/lineFileUtilities/ \
            -I$(UTILITIES_DIR)/gzstream/ \
            -I$(UTILITIES_DIR)/fileType/ \

src/complementBed/complementBed.h

@@ -10,7 +10,7 @@
   Licenced under the GNU General Public License 2.0 license.
 ******************************************************************************/
 #include "bedFile.h"
-#include "genomeFile.h"
+#include "GenomeFile.h"
 
 #include <vector>
 #include <bitset>

src/flankBed/Makefile

@@ -6,7 +6,7 @@ BIN_DIR = ../../bin/
 # define our includes
 # -------------------
 INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
-           -I$(UTILITIES_DIR)/genomeFile/ \
+           -I$(UTILITIES_DIR)/GenomeFile/ \
            -I$(UTILITIES_DIR)/lineFileUtilities/ \
            -I$(UTILITIES_DIR)/gzstream/ \
            -I$(UTILITIES_DIR)/fileType/ \

src/flankBed/flankBed.h

@@ -11,7 +11,7 @@
 ******************************************************************************/
 
 #include "bedFile.h"
-#include "genomeFile.h"
+#include "GenomeFile.h"
 
 #include <vector>
 #include <iostream>

src/genomeCoverageBed/Makefile

@@ -7,7 +7,7 @@ BIN_DIR = ../../bin/
 # -------------------
 INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
            -I$(UTILITIES_DIR)/gzstream/ \
-           -I$(UTILITIES_DIR)/genomeFile/ \
+           -I$(UTILITIES_DIR)/GenomeFile/ \
            -I$(UTILITIES_DIR)/lineFileUtilities/ \
            -I$(UTILITIES_DIR)/fileType/ \
            -I$(UTILITIES_DIR)/BamTools/include \

src/genomeCoverageBed/genomeCoverageBed.h

@@ -10,7 +10,7 @@ aaronquinlan@gmail.com
 Licenced under the GNU General Public License 2.0 license.
 ******************************************************************************/
 #include "bedFile.h"
-#include "genomeFile.h"
+#include "GenomeFile.h"
 
 #include "BlockedIntervals.h"
 #include "api/BamReader.h"