Allow input files to have consecutive tabs (i.e., empty fields)

Makefile

@@ -50,8 +50,7 @@ SUBDIRS = $(SRC_DIR)/annotateBed \
 		  $(SRC_DIR)/windowBed \
 		  $(SRC_DIR)/windowMaker
 
-UTIL_SUBDIRS =	$(SRC_DIR)/utils/lineFileUtilities \
-				$(SRC_DIR)/utils/bedFile \
+UTIL_SUBDIRS =	$(SRC_DIR)/utils/bedFile \
 				$(SRC_DIR)/utils/bedGraphFile \
 				$(SRC_DIR)/utils/chromsweep \
 				$(SRC_DIR)/utils/gzstream \

src/bedToBam/bedToBam.cpp

@@ -254,8 +254,8 @@ void ConvertBedToBam(const BED &bed, BamAlignment &bam, map<string, int, std::le
             unsigned int blockCount = atoi(bed.fields[9].c_str());
 
             vector<int> blockSizes, blockStarts;
-            Tokenize(bed.fields[10], blockSizes, ",");
-            Tokenize(bed.fields[11], blockStarts, ",");
+            Tokenize(bed.fields[10], blockSizes, ',');
+            Tokenize(bed.fields[11], blockStarts, ',');
 
             // make sure this is a well-formed BED12 entry.
             if (blockSizes.size() != blockCount) {

src/getOverlap/getOverlap.cpp

@@ -88,7 +88,7 @@ int getoverlap_main(int argc, char* argv[]) {
         // Split the column string sent by the user into discrete column numbers
         // A comma separated string is expected.
         vector<string> posColumns;
-        Tokenize(columns, posColumns, ",");
+        Tokenize(columns, posColumns, ',');
 
         if (posColumns.size() != 4) {
             cerr << endl << "*****" << endl << "*****ERROR: Please specify 4, comma-separated position columns. " << endl << "*****" << endl;

src/groupBy/groupBy.cpp

@@ -161,7 +161,7 @@ int groupby_main(int argc, char* argv[]) {
     // split the opsString into discrete operations and make sure they are all valid.
     vector<string> ops;
     opsString.erase(remove_if(opsString.begin(),opsString.end(),::isspace),opsString.end());
-    Tokenize(opsString, ops, ",");
+    Tokenize(opsString, ops, ',');
     for( size_t i = 0; i < ops.size(); i++ ) {
         if ((ops[i] != "sum")  && (ops[i] != "max")    && (ops[i] != "min") && (ops[i] != "mean") &&
             (ops[i] != "mode") && (ops[i] != "median") && (ops[i] != "antimode") && (ops[i] != "stdev") &&
@@ -177,10 +177,10 @@ int groupby_main(int argc, char* argv[]) {
         // Split the column string sent by the user into discrete column numbers
         // A comma separated string is expected.
         vector<int> groupColumnsInt;
-        Tokenize(groupColumnsString, groupColumnsInt, ",");
+        Tokenize(groupColumnsString, groupColumnsInt, ',');
 
         vector<int> opColumnsInt;
-        Tokenize(opsColumnString, opColumnsInt, ",");
+        Tokenize(opsColumnString, opColumnsInt, ',');
 
         // sanity check the group columns
         for(size_t i = 0; i < groupColumnsInt.size(); ++i) {

src/utils/BlockedIntervals/BlockedIntervals.cpp

@@ -91,8 +91,8 @@ void GetBedBlocks(const BED &bed, bedVector &bedBlocks) {
 
         vector<int> sizes;
         vector<int> starts;
-        Tokenize(blockSizes, sizes, ",");
-        Tokenize(blockStarts, starts, ",");
+        Tokenize(blockSizes, sizes, ',');
+        Tokenize(blockStarts, starts, ',');
 
         if ( sizes.size() != (size_t) blockCount || starts.size() != (size_t) blockCount ) {
             cerr << "Input error: found interval with block-counts not matching starts/sizes on line." << endl;

src/utils/lineFileUtilities/Makefile

-OBJ_DIR = ../../../obj/
-BIN_DIR = ../../../bin/
-UTILITIES_DIR = ../../utils/
-# -------------------
-# define our includes
-# -------------------
-INCLUDES = 
-
-# ----------------------------------
-# define our source and object files
-# ----------------------------------
-SOURCES= lineFileUtilities.cpp lineFileUtilities.h
-OBJECTS= $(SOURCES:.cpp=.o)
-_EXT_OBJECTS=	
-EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
-BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
-
-$(BUILT_OBJECTS): $(SOURCES)
-	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
-
-$(EXT_OBJECTS):
-	@$(MAKE) --no-print-directory -C $(INCLUDES)
-
-clean:
-	@echo "Cleaning up."
-	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
-
-.PHONY: clean
\ No newline at end of file

src/utils/lineFileUtilities/lineFileUtilities.cpp

-//
-//  lineFileUtilities.cpp
-//  BEDTools
-//
-//  Created by Aaron Quinlan Spring 2009.
-//  Copyright 2009 Aaron Quinlan. All rights reserved.
-//
-//  Summary:  Contains common functions for processing text files.
-//
-#include <sstream>
-#include <iostream>
-#include "lineFileUtilities.h"
-
-
-

src/utils/lineFileUtilities/lineFileUtilities.h

@@ -6,6 +6,7 @@
 #include <cstring>
 #include <cstdlib>
 #include <sstream>
+#include <iostream>
 
 using namespace std;
 
@@ -20,31 +21,28 @@ std::string ToString(const T & value) {
 
 // tokenize into a list of strings.
 inline
-void Tokenize(const string &str, vector<string> &elems, const string &delimiter = "\t") 
+void Tokenize(const string &str, vector<string> &elems, char delimiter = '\t') 
 {
-    char* tok;
-    char cchars [str.size()+1];
-    char* cstr = &cchars[0];
-    strcpy(cstr, str.c_str());
-    tok = strtok(cstr, delimiter.c_str());
-    while (tok != NULL) {
-        elems.push_back(tok);
-        tok = strtok(NULL, delimiter.c_str());
+    // http://stackoverflow.com/questions/236129/how-to-split-a-string-in-c/236803#236803
+    // NOTE: this approach intentionally allows consecutive delimiters
+    std::stringstream ss(str);
+    std::string item;
+    while(getline(ss, item, delimiter)) {
+        elems.push_back(item);  
     }
 }
 
 // tokenize into a list of integers
 inline
-void Tokenize(const string &str, vector<int> &elems, const string &delimiter = "\t") 
+void Tokenize(const string &str, vector<int> &elems, char delimiter = '\t') 
 {
-    char* tok;
-    char cchars [str.size()+1];
-    char* cstr = &cchars[0];
-    strcpy(cstr, str.c_str());
-    tok = strtok(cstr, delimiter.c_str());
-    while (tok != NULL) {
-        elems.push_back(atoi(tok));
-        tok = strtok(NULL, delimiter.c_str());
+
+    // http://stackoverflow.com/questions/236129/how-to-split-a-string-in-c/236803#236803
+    // NOTE: this approach intentionally allows consecutive delimiters
+    std::stringstream ss(str);
+    std::string item;
+    while(getline(ss, item, delimiter)) {
+        elems.push_back(atoi(item.c_str()));  
     }
 }