Examples of org.broad.igv.tools.parsers.ToolsWiggleParser

org.broad.igv.tools.parsers.ToolsWiggleParser
e.ucsc.edu/goldenPath/help/wiggle.html The data read in is added to a {@link DataConsumer}




    public static void main(String[] args) throws IOException {
        String input =  args[0]; //"/Users/jrobinso/Sigma/566.wgs.bam.large_isize.wig";
        WigToBed wigToBed = new WigToBed(input, .17f, .55f);
        ToolsWiggleParser parser = new ToolsWiggleParser(input, wigToBed, null);
        parser.parse();
    }

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        upperName =  String.valueOf((int) (homThreshold * 10));


        int len = inputFile.length();
        String outputFile = inputFile.substring(0, len - 4) + ".bed";
        WigToBed wigToBed = new WigToBed(outputFile, hetThreshold, homThreshold);
        ToolsWiggleParser parser = new ToolsWiggleParser(inputFile, wigToBed, null);
        parser.parse();
    }

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        String tmp = (typeString == null ? iFile.getAbsolutePath() : typeString).toLowerCase();
        if (tmp.endsWith(".txt")) tmp = tmp.substring(0, tmp.length() - 4);
        if (tmp.endsWith(".gz")) tmp = tmp.substring(0, tmp.length() - 3);
        if (tmp.endsWith("wig") || tmp.endsWith("bedgraph") || tmp.endsWith("cpg") || tmp.endsWith("map")) {
            ToolsWiggleParser wg = new ToolsWiggleParser(iFile.getAbsolutePath(), this, genome);
            wg.parse();
        } else if (tmp.endsWith("cn") || tmp.endsWith("xcn") || tmp.endsWith("igv") || tmp.endsWith("snp")) {
            CNParser cnParser = new CNParser(iFile.getAbsolutePath(), this, genome);
            cnParser.parse();
        } else {
            String msg = "Error: cannot convert files of type '" + tmp + "' to TDF format.";

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