Mercurial > repos > timpalpant > java_genomics_toolkit
view src/edu/unc/genomics/wigmath/LogTransform.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 LogTransform extends WigMathTool { private static final Logger log = Logger.getLogger(LogTransform.class); @Parameter(names = {"-i", "--input"}, description = "Input file", required = true) public WigFile inputFile; @Parameter(names = {"-b", "--base"}, description = "Logarithm base (default = 2)") public double base = 2; private double baseChange; @Override public void setup() { baseChange = Math.log(base); inputs.add(inputFile); } @Override public float[] compute(String chr, int start, int stop) throws IOException, WigFileException { log.debug("Computing difference for chunk "+chr+":"+start+"-"+stop); Iterator<WigItem> data = inputFile.query(chr, start, stop); float[] result = WigFile.flattenData(data, start, stop); for (int i = 0; i < result.length; i++) { result[i] = (float) (Math.log(result[i]) / baseChange); } return result; } /** * @param args * @throws WigFileException * @throws IOException */ public static void main(String[] args) throws IOException, WigFileException { new LogTransform().instanceMain(args); } }