--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/edu/unc/genomics/nucleosomes/FindBoundaryNucleosomes.java	Mon Feb 13 22:12:06 2012 -0500
@@ -0,0 +1,98 @@
+package edu.unc.genomics.nucleosomes;
+
+import java.io.BufferedWriter;
+import java.io.IOException;
+import java.nio.charset.Charset;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+
+import com.beust.jcommander.Parameter;
+
+import edu.unc.genomics.CommandLineTool;
+import edu.unc.genomics.Interval;
+import edu.unc.genomics.ReadablePathValidator;
+import edu.unc.genomics.io.IntervalFile;
+
+public class FindBoundaryNucleosomes extends CommandLineTool {
+	
+	private static final Logger log = Logger.getLogger(FindBoundaryNucleosomes.class);
+
+	@Parameter(names = {"-i", "--input"}, description = "Input file (nucleosome calls)", required = true, validateWith = ReadablePathValidator.class)
+	public Path inputFile;
+	@Parameter(names = {"-l", "--loci"}, description = "Boundary loci (Bed format)", required = true)
+	public IntervalFile<? extends Interval> lociFile;
+	@Parameter(names = {"-o", "--output"}, description = "Output file", required = true)
+	public Path outputFile;
+	
+	private Map<String,List<NucleosomeCall>> nucs = new HashMap<>();
+	
+	private List<NucleosomeCall> getIntervalNucleosomes(Interval i) {
+		List<NucleosomeCall> intervalNucs = new ArrayList<>();
+		for (NucleosomeCall call : nucs.get(i.getChr())) {
+			if (call.getDyad() >= i.low() && call.getDyad() <= i.high()) {
+				intervalNucs.add(call);
+			}
+		}
+		
+		return intervalNucs;
+	}
+	
+	@Override
+	public void run() throws IOException {		
+		log.debug("Initializing input file");
+		NucleosomeCallsFile nucsFile = new NucleosomeCallsFile(inputFile);
+		log.debug("Loading all nucleosomes");
+		for (NucleosomeCall nuc : nucsFile) {
+			if (nuc == null) continue;
+			if (!nucs.containsKey(nuc.getChr())) {
+				nucs.put(nuc.getChr(), new ArrayList<NucleosomeCall>());
+			}
+			nucs.get(nuc.getChr()).add(nuc);
+		}
+		nucsFile.close();
+		
+		log.debug("Initializing output file");
+		int skipped = 0;
+		try (BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) {
+			log.debug("Finding boundary nucleosomes for each interval");
+			NucleosomeCall.DyadComparator comparator = new NucleosomeCall.DyadComparator();
+			for (Interval interval : lociFile) {
+				writer.write(interval.toBed());
+				
+				// Get all of the nucleosomes within this interval
+				List<NucleosomeCall> intervalNucs = getIntervalNucleosomes(interval);
+	
+				if (intervalNucs.size() > 0) {
+					// Sort the list by nucleosome position
+					Collections.sort(intervalNucs, comparator);
+					if (interval.isCrick()) {
+						Collections.reverse(intervalNucs);
+					}
+					
+					int fivePrime = intervalNucs.get(0).getDyad();
+					int threePrime = intervalNucs.get(intervalNucs.size()-1).getDyad();
+					writer.write("\t"+fivePrime+"\t"+threePrime);
+				} else {
+					skipped++;
+					writer.write("\tNA\tNA");
+				}
+				
+				writer.newLine();
+			}
+		}
+		
+		lociFile.close();
+		log.info("Skipped "+skipped+" intervals with 0 nucleosomes");
+	}
+	
+	public static void main(String[] args) {
+		new FindBoundaryNucleosomes().instanceMain(args);
+	}
+}
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