Package org.broad.igv.tools.parsers

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


        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.";
            msg += "\nTry specifying the file type with the --fileType parameter.";
            throw new RuntimeException(msg);
        }
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Related Classes of org.broad.igv.tools.parsers.CNParser

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