org.snpeff.ped.PedFileIterator Maven / Gradle / Ivy

Go to download

Show more of this group Show more artifacts with this name
Show all versions of SnpEff Show documentation

Variant annotation and effect prediction package.

The newest version!

package org.snpeff.ped;

import java.io.IOException;

import org.snpeff.fileIterator.FileIterator;

/**
 * PED file iterator (PED file from PLINK)
 * 
 * Reference: http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml
 * 
 * @author pcingola
 */
public class PedFileIterator extends FileIterator {

	PlinkMap plinkMap;

	public PedFileIterator(String fileName, String mapFileName) {
		super(fileName);
		plinkMap = new PlinkMap();
		plinkMap.read(mapFileName);
	}

	public PlinkMap getPlinkMap() {
		return plinkMap;
	}

	/**
	 * Parse one line
	 * @param line
	 * @return
	 */
	PedEntry parseLine(String line) {
		return new PedEntry(plinkMap, line);
	}

	@Override
	protected PedEntry readNext() {
		try {
			if (reader.ready()) {
				line = reader.readLine(); // Read a line (only if needed)
				if (line != null) {
					lineNum++;
					try {
						PedEntry pedEntry = parseLine(line);
						if (pedEntry != null) return pedEntry;
					} catch (Throwable t) {
						throw new RuntimeException("Error parsing line from PED/TFAM file:\n\tFile name : '" + fileName + "'\n\tLine number : " + lineNum + "\n\tLine: '" + line + "'", t);
					};

				}
			}
		} catch (IOException e) {
			return null;
		}

		return null;
	}
}