Mercurial > repos > timpalpant > java_genomics_toolkit
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/src/edu/unc/genomics/wigmath/Subtract.java Mon Feb 13 22:12:06 2012 -0500 @@ -0,0 +1,61 @@ +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); + } + +}