Mercurial > repos > timpalpant > java_genomics_toolkit
view src/edu/unc/genomics/wigmath/Divide.java @ 2:e16016635b2a
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author | timpalpant |
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date | Mon, 13 Feb 2012 22:12:06 -0500 |
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package edu.unc.genomics.wigmath; import java.io.IOException; import java.util.Iterator; import org.apache.log4j.Logger; import org.broad.igv.bbfile.WigItem; import com.beust.jcommander.Parameter; import edu.unc.genomics.io.WigFile; import edu.unc.genomics.io.WigFileException; public class Divide extends WigMathTool { private static final Logger log = Logger.getLogger(Divide.class); @Parameter(names = {"-n", "--numerator"}, description = "Dividend / Numerator (file 1)", required = true) public WigFile dividendFile; @Parameter(names = {"-d", "--denominator"}, description = "Divisor / Denominator (file 2)", required = true) public WigFile divisorFile; @Override public void setup() { inputs.add(dividendFile); inputs.add(divisorFile); log.debug("Initialized " + inputs.size() + " input files"); } @Override public float[] compute(String chr, int start, int stop) throws IOException, WigFileException { log.debug("Computing difference for chunk "+chr+":"+start+"-"+stop); Iterator<WigItem> dividendData = dividendFile.query(chr, start, stop); Iterator<WigItem> divisorData = divisorFile.query(chr, start, stop); float[] result = WigFile.flattenData(dividendData, start, stop); while (divisorData.hasNext()) { WigItem item = divisorData.next(); for (int i = item.getStartBase(); i <= item.getEndBase(); i++) { if (i-start >= 0 && i-start < result.length) { if (item.getWigValue() != 0) { result[i-start] /= item.getWigValue(); } else { result[i-start] = Float.NaN; } } } } return result; } /** * @param args * @throws WigFileException * @throws IOException */ public static void main(String[] args) throws IOException, WigFileException { new Divide().instanceMain(args); } }