org.snpeff.outputFormatter.BedOutputFormatter 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.outputFormatter;

import java.util.HashSet;

import org.snpeff.interval.Marker;
import org.snpeff.interval.Variant;
import org.snpeff.snpEffect.VariantEffect;

/**
 * Formats output as BED file
 * 
 * Referneces: http://genome.ucsc.edu/FAQ/FAQformat.html#format1
 * 
 * @author pcingola
 */
public class BedOutputFormatter extends OutputFormatter {

	public BedOutputFormatter() {
		super();
		outOffset = 0; // Bed format is zero-based
	}

	/**
	 * Finish up section
	 * @param marker
	 */
	@Override
	public String endSection(Marker marker) {
		// Ignore other markers (e.g. seqChanges)
		if (marker instanceof Variant) return super.endSection(marker);
		return null;
	}

	@Override
	public void setOutOffset(int outOffset) {
		throw new RuntimeException("Cannot set output offset on '" + this.getClass().getSimpleName() + "' formatter!");
	}

	@Override
	public void startSection(Marker marker) {
		// Ignore other markers (e.g. seqChanges)
		if (marker instanceof Variant) super.startSection(marker);
	}

	/**
	 * Show all effects
	 */
	@Override
	public String toString() {
		Variant seqChange = (Variant) section;

		// Show results
		HashSet chEffs = new HashSet();
		for (VariantEffect varEff : variantEffects) {
			// If it is not filtered out by changeEffectResutFilter  => Show it
			if ((variantEffectResutFilter == null) || (!variantEffectResutFilter.filter(varEff))) {

				StringBuffer sb = new StringBuffer();
				sb.append(varEff.effect(true, false, false, useSequenceOntology, false));

				Marker m = varEff.getMarker();
				if (m != null) chEffs.add(m.idChain("|", ":", useGeneId, varEff));
			}

		}

		StringBuilder changeEffSb = new StringBuilder();
		changeEffSb.append(seqChange.getId()); // Start with the old 'name' field
		for (String chEff : chEffs) {
			changeEffSb.append(";");
			changeEffSb.append(chEff);
		}

		return chrStr + seqChange.getChromosomeName() //
				+ "\t" + (seqChange.getStart() + outOffset) //
				+ "\t" + (seqChange.getEnd() + 1) // End base is not included in BED format
				+ "\t" + changeEffSb.toString() //
		// + "\t" + (!Double.isNaN(seqChange.getScore()) ? seqChange.getScore() : "") //
		;
	}

	/**
	 * Show header
	 */
	@Override
	public String toStringHeader() {
		return "# SnpEff version " + version + "\n" //
				+ "# Command line: " + commandLineStr + "\n" //
				+ "# Chromo\tStart\tEnd\tName;Effect|Gene|BioType\tScore"; //
	}
}