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AlignmentFileQualityControl.java
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AlignmentFileQualityControl.java
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package org.opencb.opencga.core.models.alignment;
import org.opencb.biodata.formats.alignment.picard.HsMetrics;
import org.opencb.biodata.formats.alignment.samtools.SamtoolsFlagstats;
import org.opencb.biodata.formats.alignment.samtools.SamtoolsStats;
import org.opencb.biodata.formats.sequence.fastqc.FastQcMetrics;
import java.io.Serializable;
public class AlignmentFileQualityControl implements Serializable {
private FastQcMetrics fastQcMetrics;
private SamtoolsStats samtoolsStats;
private SamtoolsFlagstats samtoolsFlagStats;
private HsMetrics hsMetrics;
public AlignmentFileQualityControl() {
this(null, null, null, null);
}
public AlignmentFileQualityControl(FastQcMetrics fastQcMetrics, SamtoolsStats samtoolsStats, SamtoolsFlagstats samtoolsFlagStats,
HsMetrics hsMetrics) {
this.fastQcMetrics = fastQcMetrics;
this.samtoolsStats = samtoolsStats;
this.samtoolsFlagStats = samtoolsFlagStats;
this.hsMetrics = hsMetrics;
}
@Override
public String toString() {
final StringBuilder sb = new StringBuilder("Alignment{");
sb.append("fastQcMetrics=").append(fastQcMetrics);
sb.append(", samtoolsStats=").append(samtoolsStats);
sb.append(", samtoolsFlagStats=").append(samtoolsFlagStats);
sb.append(", hsMetrics=").append(hsMetrics);
sb.append('}');
return sb.toString();
}
public FastQcMetrics getFastQcMetrics() {
return fastQcMetrics;
}
public AlignmentFileQualityControl setFastQcMetrics(FastQcMetrics fastQcMetrics) {
this.fastQcMetrics = fastQcMetrics;
return this;
}
public SamtoolsStats getSamtoolsStats() {
return samtoolsStats;
}
public AlignmentFileQualityControl setSamtoolsStats(SamtoolsStats samtoolsStats) {
this.samtoolsStats = samtoolsStats;
return this;
}
public SamtoolsFlagstats getSamtoolsFlagStats() {
return samtoolsFlagStats;
}
public AlignmentFileQualityControl setSamtoolsFlagStats(SamtoolsFlagstats samtoolsFlagStats) {
this.samtoolsFlagStats = samtoolsFlagStats;
return this;
}
public HsMetrics getHsMetrics() {
return hsMetrics;
}
public AlignmentFileQualityControl setHsMetrics(HsMetrics hsMetrics) {
this.hsMetrics = hsMetrics;
return this;
}
}