Qsnp qio

qcommon/src/org/qcmg/common/model/QSnpRecord.java

@@ -0,0 +1,107 @@
+/**
+ * © Copyright The University of Queensland 2010-2014.
+ * © Copyright QIMR Berghofer Medical Research Institute 2014-2016.
+ *
+ * This code is released under the terms outlined in the included LICENSE file.
+ */
+package org.qcmg.common.model;
+
+import org.qcmg.common.vcf.VcfRecord;
+
+@Deprecated
+public class QSnpRecord {
+
+	private final VcfRecord vcf;
+	private String alt;
+	private GenotypeEnum controlGenotype;
+	private GenotypeEnum testGenotype;
+	private Accumulator control;
+	private Accumulator test;
+	private int normalNovelStartCount;
+	private int tumourNovelStartCount;
+	private Classification classification;
+	private String flankingSequence;
+
+	public QSnpRecord(VcfRecord vcf) {
+		this.vcf = vcf;
+	}
+
+	public QSnpRecord(String chr, int position, String ref) {
+		this(chr, position, ref, null);
+	}
+	public QSnpRecord(String chr, int position, String ref, String alt) {
+		vcf = new VcfRecord.Builder(chr, position, ref).allele(alt).build();
+
+	}
+	public void setAlt(String alt) {
+		this.alt = alt;
+	}
+
+	public ChrPosition getChrPos() {
+		return vcf.getChrPosition();
+	}
+
+	public String getRef() {
+		return vcf.getRef();
+	}
+	public String getAlt() {
+		return null != vcf.getAlt() ? vcf.getAlt() : alt;
+	}
+	public String getChromosome() {
+		return vcf.getChromosome();
+	}
+	public int getPosition() {
+		return vcf.getPosition();
+	}
+	public GenotypeEnum getNormalGenotype() {
+		return controlGenotype;
+	}
+	public void setNormalGenotype(GenotypeEnum normalGenotype) {
+		this.controlGenotype = normalGenotype;
+	}
+	public GenotypeEnum getTumourGenotype() {
+		return testGenotype;
+	}
+	public void setTumourGenotype(GenotypeEnum tumourGenotype) {
+		this.testGenotype = tumourGenotype;
+	}
+	public void setClassification(Classification classification) {
+		this.classification = classification;
+	}
+	public Classification getClassification() {
+		return classification;
+	}
+
+	public String getAnnotation() {
+		return vcf.getFilter();
+	}
+
+	public String getUnfilteredNormalPileup() {
+		return null != control ? control.getFailedFilterPileup() : null;
+	}
+	public int getNovelStartCount() {
+		return Classification.GERMLINE != classification ? tumourNovelStartCount : normalNovelStartCount;
+	}
+	public void setNormalNovelStartCount(int normalNovelStartCount) {
+		this.normalNovelStartCount = normalNovelStartCount;
+	}
+	public int getNormalNovelStartCount() {
+		return normalNovelStartCount;
+	}
+	public void setTumourNovelStartCount(int tumourNovelStartCount) {
+		this.tumourNovelStartCount = tumourNovelStartCount;
+	}
+	public int getTumourNovelStartCount() {
+		return tumourNovelStartCount;
+	}
+	public void setFlankingSequence(String flankingSequence) {
+		this.flankingSequence = flankingSequence;
+	}
+	public String getFlankingSequence() {
+		return flankingSequence;
+	}
+
+	public VcfRecord getVcfRecord() {
+		return vcf;
+	}
+}

qio/test/org/qcmg/pileup/QSnpRecordTest.java → qcommon/test/org/qcmg/common/model/QSnpRecordTest.java

@@ -1,4 +1,4 @@
-package org.qcmg.pileup;
+package org.qcmg.common.model;
 
 import static org.junit.Assert.assertEquals;
 

qio/src/org/qcmg/pileup/QPileupFileReader.java

@@ -9,6 +9,7 @@
 import java.io.IOException;
 import java.io.InputStream;
 import java.util.Iterator;
+import org.qcmg.common.model.QSnpRecord;
 
 public final class QPileupFileReader implements Closeable, Iterable<QSnpRecord> {
     private final File file;

qio/src/org/qcmg/pileup/QPileupRecordIterator.java

@@ -8,6 +8,7 @@
 import java.io.InputStreamReader;
 import java.util.Iterator;
 import java.util.NoSuchElementException;
+import org.qcmg.common.model.QSnpRecord;
 
 public final class QPileupRecordIterator implements Iterator<QSnpRecord> {
     private final BufferedReader reader;

qio/src/org/qcmg/pileup/QPileupSerializer.java

@@ -13,6 +13,7 @@
 import org.qcmg.common.model.Classification;
 import org.qcmg.common.util.BaseUtils;
 import org.qcmg.common.model.Classification;
+import org.qcmg.common.model.QSnpRecord;
 
 public final class QPileupSerializer {
 	private static final Pattern tabbedPattern = Pattern.compile("[\\t]");