org.snpeff.fastq.FastqTrimmerMedian 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.fastq;

import java.util.Collections;
import java.util.LinkedList;

/**
 * Trim fastq sequence when median quality drops below a threshold
 * 
 * @author pcingola
 *
 */
public class FastqTrimmerMedian extends FastqTrimmer {

	int runningMedianLength; // How many bases do we consider for calculating the median 

	public FastqTrimmerMedian(int qualityThreshold, int minBases, int runningMedianLength) {
		super(qualityThreshold, minBases);
		this.runningMedianLength = runningMedianLength;
	}

	/**
	 * Calculate the running median
	 * @return
	 */
	int median(int qual[], int i) {
		// Create a list
		LinkedList list = new LinkedList();
		for( int k = 0, j = i - runningMedianLength + 1; k < runningMedianLength; k++, j++ )
			if( (j >= 0) && (j < qual.length) ) list.add(qual[j]);
		Collections.sort(list);

		int size = list.size(), med = 0;
		if( list.size() % 2 == 1 ) med = list.get(size / 2);
		else med = (list.get(size / 2 - 1) + list.get(size / 2)) / 2;

		return med;
	}

	/**
	 * Return index where the sequence should be trimmed
	 * First time quality median drops below 'qualityThreshold'
	 */
	@Override
	int trimIndex(Fastq fastq) {
		int qual[] = FastqTools.qualtityArray(fastq);

		for( int i = 0; i < qual.length; i++ ) {
			int median = median(qual, i); // Compute running median
			if( median < qualityThreshold ) return i; // Below threshold? => trim here
		}

		return qual.length;
	}
}