diff --git a/Makefile b/Makefile
index 735ceb9cdeb995a0cb812bd99de9445692fb5c24..167fc1e8035bfdb8c9ebbc15abfd9f1d7080fe7a 100644
--- a/Makefile
+++ b/Makefile
@@ -44,7 +44,8 @@ SUBDIRS = $(SRC_DIR)/annotateBed \
$(SRC_DIR)/subtractBed \
$(SRC_DIR)/tagBam \
$(SRC_DIR)/unionBedGraphs \
- $(SRC_DIR)/windowBed
+ $(SRC_DIR)/windowBed \
+ $(SRC_DIR)/windowMaker
UTIL_SUBDIRS = $(SRC_DIR)/utils/lineFileUtilities \
$(SRC_DIR)/utils/bedFile \
diff --git a/scripts/makeBashScripts.py b/scripts/makeBashScripts.py
index 2345bbf50510884435a62b6337e3566e07017ddb..410f5ffb77c474772c0650c069560801fe80fe6f 100644
--- a/scripts/makeBashScripts.py
+++ b/scripts/makeBashScripts.py
@@ -37,7 +37,8 @@ def main():
'subtract': 'subtractBed',
'tag': 'tagBam',
'unionbedg': 'unionBedGraphs',
- 'window': 'windowBed'}
+ 'window': 'windowBed',
+ 'makewindows': 'windowMaker'}
# create a BASH script for each old tool, mapping to the new CLI command.
for tool in tool_map:
diff --git a/src/bedtools.cpp b/src/bedtools.cpp
index 05f849a81a293f56d623dec528741a40ba4db43a..0bcc5c2a2efe28e0d2da6bce7c6dd256c4888a08 100644
--- a/src/bedtools.cpp
+++ b/src/bedtools.cpp
@@ -63,6 +63,7 @@ int subtract_main(int argc, char* argv[]); //
int tagbam_main(int argc, char* argv[]);//
int unionbedgraphs_main(int argc, char* argv[]);//
int window_main(int argc, char* argv[]); //
+int windowmaker_main(int argc, char* argv[]); //
int bedtools_help(void);
int bedtools_faq(void);
@@ -116,6 +117,7 @@ int main(int argc, char *argv[])
else if (sub_cmd == "overlap") return getoverlap_main(argc-1, argv+1);
else if (sub_cmd == "igv") return bedtoigv_main(argc-1, argv+1);
else if (sub_cmd == "links") return links_main(argc-1, argv+1);
+ else if (sub_cmd == "makewindows") return windowmaker_main(argc-1, argv+1);
// help
else if (sub_cmd == "-h" || sub_cmd == "--help" ||
@@ -134,14 +136,16 @@ int main(int argc, char *argv[])
// verison information
else if (sub_cmd == "-contact" || sub_cmd == "--contact")
{
- cout << "For further help, please email the bedtools mailing list: " << endl;
- cout << "bedtools-discuss@googlegroups.com" << endl << endl;
+ cout << endl;
+ cout << "- For further help, or to report a bug, please " << endl;
+ cout << " email the bedtools mailing list: " << endl;
+ cout << " bedtools-discuss@googlegroups.com" << endl << endl;
- cout << "Stable releases of bedtools can be found at: " << endl;
- cout << "http://bedtools.googlecode.com" << endl << endl;
+ cout << "- Stable releases of bedtools can be found at: " << endl;
+ cout << " http://bedtools.googlecode.com" << endl << endl;
- cout << "The development repository can be found at: " << endl;
- cout << "https://github.com/arq5x/bedtools" << endl << endl;
+ cout << "- The development repository can be found at: " << endl;
+ cout << " https://github.com/arq5x/bedtools" << endl << endl;
}
// unknown
else {
@@ -208,11 +212,12 @@ int bedtools_help(void)
cout << " overlap " << "Computes the amount of overlap from two intervals.\n";
cout << " igv " << "Create an IGV snapshot batch script.\n";
cout << " links " << "Create a HTML page of links to UCSC locations.\n";
+ cout << " makewindows " << "Make interval \"windows\" across a genome.\n";
cout << endl;
cout << " -General help:\n";
cout << " --help " << "Print this help menu.\n";
- cout << " --faq " << "Frequently asked questions.\n";
+ //cout << " --faq " << "Frequently asked questions.\n"; TODO
cout << " --version " << "What version of bedtools are you using?.\n";
cout << " --contact " << "Feature requests, bugs, mailing lists, etc.\n";
diff --git a/src/windowMaker/Makefile b/src/windowMaker/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..ea27b299e58af92305f3964327436873556721ae
--- /dev/null
+++ b/src/windowMaker/Makefile
@@ -0,0 +1,37 @@
+UTILITIES_DIR = ../utils/
+OBJ_DIR = ../../obj/
+BIN_DIR = ../../bin/
+
+# -------------------
+# define our includes
+# -------------------
+INCLUDES = -I$(UTILITIES_DIR)/genomeFile/ \
+ -I$(UTILITIES_DIR)/BamTools/include
+
+# ----------------------------------
+# define our source and object files
+# ----------------------------------
+SOURCES= windowMakerMain.cpp windowMaker.cpp
+OBJECTS= $(SOURCES:.cpp=.o)
+_EXT_OBJECTS=genomeFile.o
+EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
+BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
+PROGRAM= windowMaker
+
+
+all: $(BUILT_OBJECTS)
+
+.PHONY: all
+
+$(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+ @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+
+$(EXT_OBJECTS):
+ @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/genomeFile/
+
+clean:
+ @echo "Cleaning up."
+ @rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
+
+.PHONY: clean
diff --git a/src/windowMaker/windowMaker.cpp b/src/windowMaker/windowMaker.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..31c9cba307a283e388ceab4cb8366b3452d130c3
--- /dev/null
+++ b/src/windowMaker/windowMaker.cpp
@@ -0,0 +1,46 @@
+/*****************************************************************************
+ windowMaker.cpp
+
+ (c) 2009 - Aaron Quinlan
+ Hall Laboratory
+ Department of Biochemistry and Molecular Genetics
+ University of Virginia
+ aaronquinlan@gmail.com
+
+ Licenced under the GNU General Public License 2.0 license.
+******************************************************************************/
+#include "windowMaker.h"
+
+WindowMaker::WindowMaker(string &genomeFile, uint32_t size, uint32_t step)
+ : _genomeFile(genomeFile)
+ , _size(size)
+ , _step(step)
+{
+ _genome = new GenomeFile(genomeFile);
+ MakeWindows();
+}
+
+WindowMaker::~WindowMaker(void) {}
+
+
+void WindowMaker::MakeWindows() {
+
+ // get a list of the chroms in the user's genome
+ vector<string> chromList = _genome->getChromList();
+
+ // process each chrom in the genome
+ for (size_t c = 0; c < chromList.size(); ++c) {
+ string chrom = chromList[c];
+ uint32_t chrom_size = _genome->getChromSize(chrom);
+
+ for (uint32_t start = 0; start <= chrom_size; start += _step) {
+ if ((start + _size) <= chrom_size) {
+ cout << chrom << "\t" << start << "\t" << start + _size << endl;
+ }
+ else if (start < chrom_size) {
+ cout << chrom << "\t" << start << "\t" << chrom_size << endl;
+ }
+ }
+ }
+}
+
diff --git a/src/windowMaker/windowMaker.h b/src/windowMaker/windowMaker.h
new file mode 100644
index 0000000000000000000000000000000000000000..29430cab8fc7121633be90d396cd8b5633d7162e
--- /dev/null
+++ b/src/windowMaker/windowMaker.h
@@ -0,0 +1,37 @@
+/*****************************************************************************
+ windowMaker.h
+
+ (c) 2009 - Aaron Quinlan
+ Hall Laboratory
+ Department of Biochemistry and Molecular Genetics
+ University of Virginia
+ aaronquinlan@gmail.com
+
+ Licenced under the GNU General Public License 2.0 license.
+******************************************************************************/
+#include "genomeFile.h"
+
+using namespace std;
+
+
+//************************************************
+// Class methods and elements
+//************************************************
+class WindowMaker {
+
+public:
+
+ // constructor
+ WindowMaker(string &genomeFile, uint32_t size, uint32_t step);
+
+ // destructor
+ ~WindowMaker(void);
+
+ void MakeWindows();
+
+private:
+ string _genomeFile;
+ GenomeFile *_genome;
+ uint32_t _size;
+ uint32_t _step;
+};
diff --git a/src/windowMaker/windowMakerMain.cpp b/src/windowMaker/windowMakerMain.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..19caf42bec3c6439e896ca663fc2a1f6b51c2f90
--- /dev/null
+++ b/src/windowMaker/windowMakerMain.cpp
@@ -0,0 +1,130 @@
+/*****************************************************************************
+ windowMakerMain.cpp
+
+ (c) 2009 - Aaron Quinlan
+ Hall Laboratory
+ Department of Biochemistry and Molecular Genetics
+ University of Virginia
+ aaronquinlan@gmail.com
+
+ Licenced under the GNU General Public License 2.0 license.
+******************************************************************************/
+#include "windowMaker.h"
+
+using namespace std;
+
+// define our program name
+#define PROGRAM_NAME "bedtools makewindows"
+
+
+// define our parameter checking macro
+#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)
+
+// function declarations
+void windowmaker_help(void);
+
+int windowmaker_main(int argc, char* argv[]) {
+
+ // our configuration variables
+ bool showHelp = false;
+
+ // input files
+ string genomeFile;
+
+ // parms
+ uint32_t size = 0;
+ uint32_t step = 0;
+
+ bool haveGenome = false;
+ bool haveSize = false;
+
+ for(int i = 1; i < argc; i++) {
+ int parameterLength = (int)strlen(argv[i]);
+
+ if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
+ (PARAMETER_CHECK("--help", 5, parameterLength))) {
+ showHelp = true;
+ }
+ }
+
+ if(showHelp) windowmaker_help();
+
+ // do some parsing (all of these parameters require 2 strings)
+ for(int i = 1; i < argc; i++) {
+
+ int parameterLength = (int)strlen(argv[i]);
+
+ if(PARAMETER_CHECK("-g", 2, parameterLength)) {
+ if ((i+1) < argc) {
+ haveGenome = true;
+ genomeFile = argv[i + 1];
+ i++;
+ }
+ }
+ else if(PARAMETER_CHECK("-w", 2, parameterLength)) {
+ if ((i+1) < argc) {
+ haveSize = true;
+ size = atoi(argv[i + 1]);
+ step = size;
+ i++;
+ }
+ }
+ else if(PARAMETER_CHECK("-s", 2, parameterLength)) {
+ if ((i+1) < argc) {
+ step = atoi(argv[i + 1]);
+ i++;
+ }
+ }
+ else {
+ cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
+ showHelp = true;
+ }
+ }
+
+ // make sure we have both input files
+ if (!haveGenome || !haveSize) {
+ cerr << endl << "*****" << endl << "*****ERROR: Need -g (genome file) and -w (window size). " << endl << "*****" << endl;
+ showHelp = true;
+ }
+ if (!showHelp) {
+ WindowMaker *wm = new WindowMaker(genomeFile, size, step);
+ delete wm;
+ }
+ else {
+ windowmaker_help();
+ }
+ return 0;
+}
+
+void windowmaker_help(void) {
+
+ cerr << "\nTool: bedtools makewindows" << endl;
+
+ cerr << "Summary: Makes adjacent and/or sliding windows across a genome." << endl << endl;
+
+ cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -g <genome> -w <window_size>" << endl << endl;
+
+ cerr << "Options: " << endl;
+
+ cerr << "\t-s\t" << "Step size: i.e., how many base pairs to step before" << endl;
+ cerr << "\t\tcreating a new window. Used to create \"sliding\" windows." << endl;
+ cerr << "\t\t- Defaults to -w (non-sliding windows)." << endl << endl;
+
+ cerr << "Notes: " << endl;
+ cerr << "\t(1) The genome file should tab delimited and structured as follows:" << endl;
+ cerr << "\t <chromName><TAB><chromSize>" << endl << endl;
+ cerr << "\tFor example, Human (hg19):" << endl;
+ cerr << "\tchr1\t249250621" << endl;
+ cerr << "\tchr2\t243199373" << endl;
+ cerr << "\t..." << endl;
+ cerr << "\tchr18_gl000207_random\t4262" << endl << endl;
+
+ cerr << "Tips: " << endl;
+ cerr << "\tOne can use the UCSC Genome Browser's MySQL database to extract" << endl;
+ cerr << "\tchromosome sizes. For example, H. sapiens:" << endl << endl;
+ cerr << "\tmysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \\" << endl;
+ cerr << "\t\"select chrom, size from hg19.chromInfo\" > hg19.genome" << endl << endl;
+
+ exit(1);
+
+}