org.snpeff.fileIterator.GenericMarkerFileIterator 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.fileIterator;

import java.io.IOException;

import org.snpeff.interval.Chromosome;
import org.snpeff.interval.GenericMarker;

/**
 * Opens a file and creates generic markers (one per line)
 *     
 * @author pcingola
 */
public class GenericMarkerFileIterator extends MarkerFileIterator {

	int colChr = 0;
	int colStart = 1;
	int colEnd = 2;

	public GenericMarkerFileIterator(String fileName, int colChr, int colStart, int colEnd, int inOffset) {
		super(fileName, inOffset);
		this.colChr = colChr;
		this.colStart = colStart;
		this.colEnd = colEnd;
	}

	@Override
	protected GenericMarker readNext() {
		// Try to read a line
		try {
			while (ready()) {
				line = readLine();

				if (line == null) return null; // End of file?

				// Ignore empty lines and comment lines
				if ((line.length() > 0) && (!line.startsWith("#"))) {
					// Parse line
					String fields[] = line.split("\\s");

					// Is line OK?
					if (fields.length >= 2) {
						// Fields 
						String chromosome = fields[colChr].trim();
						Chromosome chromo = getChromosome(chromosome);
						sanityCheckChromo(chromosome, chromo); // Sanity check

						// Start
						int start = 0;
						if (fields.length > colStart) start = parsePosition(fields[colStart]);

						// End
						int end = start;
						if (fields.length > colEnd) end = parsePosition(fields[colEnd]);

						// ID
						String id = "line_" + lineNum;
						if ((fields.length > 3) && (!fields[3].isEmpty())) id = fields[3];

						// Create genericMarker
						GenericMarker genericMarker = new GenericMarker(chromo, start, end, id);
						genericMarker.setLine(line); // Store original line
						return genericMarker;
					}
				}
			}
		} catch (IOException e) {
			throw new RuntimeException(e);
		}
		return null;
	}
}