org.opencb.biodata.tools.alignment.stats.AlignmentGlobalStats Maven / Gradle / Ivy

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/*
 * 
 *
 */

package org.opencb.biodata.tools.alignment.stats;

import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.ObjectWriter;

import java.io.IOException;
import java.util.HashMap;
import java.util.Map;

public class AlignmentGlobalStats {

	public int numMapped;
	public int numUnmapped;
	public int numPaired;
	public int numMappedFirst;
	public int numMappedSecond;

	public int NM;
	
	public int numHardC;
	public int numSoftC;
	public int numIn;
	public int numDel;
	public int numPad;
	public int numSkip;
	
	public int accMappingQuality;
	public Map mappingQualityMap;

	public int accInsert;
	public Map insertMap;

//	public long pos;
//	public List cigar;

	public SequenceStats seqStats;

	public AlignmentGlobalStats() {
		mappingQualityMap = new HashMap<> ();
		insertMap = new HashMap<> ();
		seqStats = new SequenceStats();
	}

	public String toJSON() throws IOException {
		ObjectWriter objectWriter = new ObjectMapper().writer();
		return objectWriter.writeValueAsString(this);
	}

	@Override
	public String toString() {
		final StringBuilder sb = new StringBuilder("AlignmentGlobalStats{");
		sb.append("numMapped=").append(numMapped);
		sb.append(", numUnmapped=").append(numUnmapped);
		sb.append(", numPaired=").append(numPaired);
		sb.append(", numMappedFirst=").append(numMappedFirst);
		sb.append(", numMappedSecond=").append(numMappedSecond);
		sb.append(", NM=").append(NM);
		sb.append(", numHardC=").append(numHardC);
		sb.append(", numSoftC=").append(numSoftC);
		sb.append(", numIn=").append(numIn);
		sb.append(", numDel=").append(numDel);
		sb.append(", numPad=").append(numPad);
		sb.append(", numSkip=").append(numSkip);
		sb.append(", accMappingQuality=").append(accMappingQuality);
		sb.append(", mappingQualityMap=").append(mappingQualityMap);
		sb.append(", accInsert=").append(accInsert);
		sb.append(", insertMap=").append(insertMap);
		sb.append(", seqStats=").append(seqStats);
		sb.append('}');
		return sb.toString();
	}

	public int getNumMapped() {
		return numMapped;
	}

	public AlignmentGlobalStats setNumMapped(int numMapped) {
		this.numMapped = numMapped;
		return this;
	}

	public int getNumUnmapped() {
		return numUnmapped;
	}

	public AlignmentGlobalStats setNumUnmapped(int numUnmapped) {
		this.numUnmapped = numUnmapped;
		return this;
	}

	public int getNumPaired() {
		return numPaired;
	}

	public AlignmentGlobalStats setNumPaired(int numPaired) {
		this.numPaired = numPaired;
		return this;
	}

	public int getNumMappedFirst() {
		return numMappedFirst;
	}

	public AlignmentGlobalStats setNumMappedFirst(int numMappedFirst) {
		this.numMappedFirst = numMappedFirst;
		return this;
	}

	public int getNumMappedSecond() {
		return numMappedSecond;
	}

	public AlignmentGlobalStats setNumMappedSecond(int numMappedSecond) {
		this.numMappedSecond = numMappedSecond;
		return this;
	}

	public int getNM() {
		return NM;
	}

	public AlignmentGlobalStats setNM(int NM) {
		this.NM = NM;
		return this;
	}

	public int getNumHardC() {
		return numHardC;
	}

	public AlignmentGlobalStats setNumHardC(int numHardC) {
		this.numHardC = numHardC;
		return this;
	}

	public int getNumSoftC() {
		return numSoftC;
	}

	public AlignmentGlobalStats setNumSoftC(int numSoftC) {
		this.numSoftC = numSoftC;
		return this;
	}

	public int getNumIn() {
		return numIn;
	}

	public AlignmentGlobalStats setNumIn(int numIn) {
		this.numIn = numIn;
		return this;
	}

	public int getNumDel() {
		return numDel;
	}

	public AlignmentGlobalStats setNumDel(int numDel) {
		this.numDel = numDel;
		return this;
	}

	public int getNumPad() {
		return numPad;
	}

	public AlignmentGlobalStats setNumPad(int numPad) {
		this.numPad = numPad;
		return this;
	}

	public int getNumSkip() {
		return numSkip;
	}

	public AlignmentGlobalStats setNumSkip(int numSkip) {
		this.numSkip = numSkip;
		return this;
	}

	public int getAccMappingQuality() {
		return accMappingQuality;
	}

	public AlignmentGlobalStats setAccMappingQuality(int accMappingQuality) {
		this.accMappingQuality = accMappingQuality;
		return this;
	}

	public Map getMappingQualityMap() {
		return mappingQualityMap;
	}

	public AlignmentGlobalStats setMappingQualityMap(HashMap mappingQualityMap) {
		this.mappingQualityMap = mappingQualityMap;
		return this;
	}

	public int getAccInsert() {
		return accInsert;
	}

	public AlignmentGlobalStats setAccInsert(int accInsert) {
		this.accInsert = accInsert;
		return this;
	}

	public Map getInsertMap() {
		return insertMap;
	}

	public AlignmentGlobalStats setInsertMap(HashMap insertMap) {
		this.insertMap = insertMap;
		return this;
	}

	public SequenceStats getSeqStats() {
		return seqStats;
	}

	public AlignmentGlobalStats setSeqStats(SequenceStats seqStats) {
		this.seqStats = seqStats;
		return this;
	}

}