Mercurial > repos > timpalpant > java_genomics_toolkit
view src/edu/unc/genomics/wigmath/Subtract.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 Subtract extends WigMathTool { private static final Logger log = Logger.getLogger(Subtract.class); @Parameter(names = {"-m", "--minuend"}, description = "Minuend (top - file 1)", required = true) public WigFile minuendFile; @Parameter(names = {"-s", "--subtrahend"}, description = "Subtrahend (bottom - file 2)", required = true) public WigFile subtrahendFile; @Override public void setup() { log.debug("Initializing input files"); inputs.add(minuendFile); inputs.add(subtrahendFile); 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> minuendData = minuendFile.query(chr, start, stop); Iterator<WigItem> subtrahendData = subtrahendFile.query(chr, start, stop); float[] result = WigFile.flattenData(minuendData, start, stop); while (subtrahendData.hasNext()) { WigItem item = subtrahendData.next(); for (int i = item.getStartBase(); i <= item.getEndBase(); i++) { if (i-start >= 0 && i-start < result.length) { result[i-start] -= item.getWigValue(); } } } return result; } /** * @param args * @throws WigFileException * @throws IOException */ public static void main(String[] args) throws IOException, WigFileException { new Subtract().instanceMain(args); } }