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1 package consensus;
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2
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3 import structures.ByteBuilder;
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4
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5 /**
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6 * Superclass for consensus package classes.
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7 *
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8 * @author Brian Bushnell
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9 * @date September 6, 2019
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10 *
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11 */
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12 public abstract class ConsensusObject {
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13
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14 /*--------------------------------------------------------------*/
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15 /*---------------- Methods ----------------*/
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16 /*--------------------------------------------------------------*/
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17
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18 /** Return the text representation of this object */
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19 public abstract ByteBuilder toText();
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20
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21 @Override
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22 public final String toString(){return toText().toString();}
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23
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24 /*--------------------------------------------------------------*/
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25 /*---------------- Statics ----------------*/
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26 /*--------------------------------------------------------------*/
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27
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28 static int minDepth=2;
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29 public static float MAF_sub=0.25f;
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30 public static float MAF_del=0.5f;
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31 public static float MAF_ins=0.5f;
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32 public static float MAF_noref=0.4f;
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33 static boolean onlyConvertNs=false;
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34 static boolean noIndels=false;
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35 public static float trimDepthFraction=0.0f;
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36 public static boolean trimNs=false;
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37
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38 public static boolean useMapq=false;
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39 public static boolean invertIdentity=false;
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40 public static int identityCeiling=150;
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41
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42 /*--------------------------------------------------------------*/
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43 /*---------------- Constants ----------------*/
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44 /*--------------------------------------------------------------*/
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45
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46 /* Possible types */
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47 /** Match/Sub, neutral-length node or edge to the next REF node */
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48 public static final int REF=2;
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49 /** Insertion node or edge to an insertion node */
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50 public static final int INS=1;
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51 /** Edge to a non-adjacent node */
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52 public static final int DEL=0;
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53
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54 static final String[] TYPE_NAMES={"DEL", "INS", "REF"};
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55
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56 public static boolean verbose=false;
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57
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58 }
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