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annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/clump/ReadKey.java @ 68:5028fdace37b

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planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 16:23:26 -0400
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jpayne@68 1 package clump;
jpayne@68 2
jpayne@68 3 import java.io.Serializable;
jpayne@68 4
jpayne@68 5 import hiseq.FlowcellCoordinate;
jpayne@68 6 import shared.KillSwitch;
jpayne@68 7 import shared.Tools;
jpayne@68 8 import stream.Read;
jpayne@68 9 import structures.IntList;
jpayne@68 10
jpayne@68 11 class ReadKey implements Serializable, Comparable<ReadKey> {
jpayne@68 12
jpayne@68 13 // public static ReadKey makeKeyIfNeeded(Read r){
jpayne@68 14 // if(r.obj==null){
jpayne@68 15 // return makeKey(r, true);
jpayne@68 16 // }
jpayne@68 17 // return (ReadKey)r.obj;
jpayne@68 18 // }
jpayne@68 19
jpayne@68 20 public static ReadKey makeKey(Read r, boolean setObject){
jpayne@68 21 assert(r.obj==null);
jpayne@68 22 try {
jpayne@68 23 ReadKey rk=new ReadKey(r);
jpayne@68 24 if(setObject){r.obj=rk;}
jpayne@68 25 return rk;
jpayne@68 26 } catch (OutOfMemoryError e) {
jpayne@68 27 KillSwitch.memKill(e);
jpayne@68 28 throw new RuntimeException(e);
jpayne@68 29 }
jpayne@68 30 }
jpayne@68 31
jpayne@68 32 private ReadKey(Read r){
jpayne@68 33 this(r, 0, 0, true);
jpayne@68 34 }
jpayne@68 35
jpayne@68 36 private ReadKey(Read r, long kmer_, int position_, boolean plus_){
jpayne@68 37 kmer=kmer_;
jpayne@68 38 position=position_;
jpayne@68 39 clump=null;
jpayne@68 40 assert(!r.swapped());
jpayne@68 41 flipped=false;
jpayne@68 42 kmerMinusStrand=!plus_;
jpayne@68 43
jpayne@68 44 if(Clump.opticalOnly){
jpayne@68 45 FlowcellCoordinate fc=FlowcellCoordinate.getFC();
jpayne@68 46 fc.setFrom(r.id);
jpayne@68 47 lane=fc.lane;
jpayne@68 48 tile=fc.tile;
jpayne@68 49 x=fc.x;
jpayne@68 50 y=fc.y;
jpayne@68 51 }
jpayne@68 52 // expectedErrors=r.expectedErrorsIncludingMate(true);
jpayne@68 53 }
jpayne@68 54
jpayne@68 55 protected ReadKey(){}
jpayne@68 56
jpayne@68 57 public void set(long kmer_, int position_, boolean minus_){
jpayne@68 58 setKmer(kmer_);
jpayne@68 59 setPosition(position_);
jpayne@68 60 // setClump(null);
jpayne@68 61 kmerMinusStrand=minus_;
jpayne@68 62 }
jpayne@68 63
jpayne@68 64 private long setKmer(long kmer_){
jpayne@68 65 return kmer=kmer_;
jpayne@68 66 }
jpayne@68 67
jpayne@68 68 private int setPosition(int position_){
jpayne@68 69 return position=position_;
jpayne@68 70 }
jpayne@68 71
jpayne@68 72 public Clump setClump(Clump clump_){
jpayne@68 73 return clump=clump_;
jpayne@68 74 }
jpayne@68 75
jpayne@68 76 private boolean setFlipped(boolean flipped_){
jpayne@68 77 assert(flipped!=flipped_);
jpayne@68 78 return flipped=flipped_;
jpayne@68 79 }
jpayne@68 80
jpayne@68 81 public void clear(){
jpayne@68 82 setKmer(0);
jpayne@68 83 setPosition(0);
jpayne@68 84 setClump(null);
jpayne@68 85 kmerMinusStrand=false;
jpayne@68 86 }
jpayne@68 87
jpayne@68 88 public void flip(Read r, int k){
jpayne@68 89 assert(r.swapped()==flipped);
jpayne@68 90 r.reverseComplement();
jpayne@68 91 r.setSwapped(!r.swapped());
jpayne@68 92 setFlipped(!flipped);
jpayne@68 93 if(r.length()>=k){setPosition(r.length()-position+k-2);}
jpayne@68 94 assert(r.swapped()==flipped);
jpayne@68 95 }
jpayne@68 96
jpayne@68 97 @Override
jpayne@68 98 public int compareTo(ReadKey b){
jpayne@68 99 if(kmer!=b.kmer){return kmer>b.kmer ? -1 : 1;} //Bigger kmers first...
jpayne@68 100 if(kmerMinusStrand!=b.kmerMinusStrand){return kmerMinusStrand ? 1 : -1;}
jpayne@68 101 if(position!=b.position){return position<b.position ? 1 : -1;}
jpayne@68 102 if(Clump.opticalOnly){
jpayne@68 103 if(lane!=b.lane){return lane-b.lane;}
jpayne@68 104 if(!spanTiles()){
jpayne@68 105 if(tile!=b.tile){return tile-b.tile;}
jpayne@68 106 }
jpayne@68 107 if(Clump.sortYEarly()){ //Improves speed slightly
jpayne@68 108 if(y!=b.y){return y-b.y;}
jpayne@68 109 }
jpayne@68 110 }
jpayne@68 111 // if(expectedErrors!=b.expectedErrors){
jpayne@68 112 // return expectedErrors>b.expectedErrors ? 1 : -1;//Higher quality first
jpayne@68 113 // }
jpayne@68 114 return 0;
jpayne@68 115 }
jpayne@68 116
jpayne@68 117 @Override
jpayne@68 118 public boolean equals(Object b){
jpayne@68 119 return equals((ReadKey)b, false);
jpayne@68 120 }
jpayne@68 121
jpayne@68 122 @Override
jpayne@68 123 public int hashCode() {
jpayne@68 124 int x=(int)((kmer^position)&0xFFFFFFFFL);
jpayne@68 125 return kmerMinusStrand ? -x : x;
jpayne@68 126 }
jpayne@68 127
jpayne@68 128 /** True if this physically contains b (ignoring mismatches) */
jpayne@68 129 public boolean physicallyContains(ReadKey b, int aLen, int bLen){
jpayne@68 130 if(bLen>aLen){return false;}
jpayne@68 131 if(kmer!=b.kmer){return false;}
jpayne@68 132 final int dif=position-b.position;
jpayne@68 133 int bStart=dif, bStop=dif+bLen;
jpayne@68 134 return bStart>=0 && bStop<=aLen;
jpayne@68 135 }
jpayne@68 136
jpayne@68 137 /** True if this physically contains b as a prefix or suffix (ignoring mismatches).
jpayne@68 138 * More restrictive than physicallyContains. */
jpayne@68 139 public boolean physicalAffix(ReadKey b, int aLen, int bLen){
jpayne@68 140 if(bLen>aLen){return false;}
jpayne@68 141 if(kmer!=b.kmer){return false;}
jpayne@68 142 final int dif=position-b.position;
jpayne@68 143 int bStart=dif, bStop=dif+bLen;
jpayne@68 144 return (bStart==0 || bStop==aLen) && bStart>=0 && bStop<=aLen;
jpayne@68 145 }
jpayne@68 146
jpayne@68 147 /** Note that this is different than compareTo()==0
jpayne@68 148 * That's to prevent sortYEarly comparison making things unequal.
jpayne@68 149 * @param b
jpayne@68 150 * @return True if equal
jpayne@68 151 */
jpayne@68 152 public boolean equals(ReadKey b, boolean containment){
jpayne@68 153 if(b==null){return false;}
jpayne@68 154 if(kmer!=b.kmer){return false;}
jpayne@68 155 if(!containment && (kmerMinusStrand!=b.kmerMinusStrand || position!=b.position)){return false;}
jpayne@68 156 if(Clump.opticalOnly){
jpayne@68 157 if(lane!=b.lane){return false;}
jpayne@68 158 if(!spanTiles()){
jpayne@68 159 if(tile!=b.tile){return false;}
jpayne@68 160 }
jpayne@68 161 }
jpayne@68 162 return true;
jpayne@68 163 }
jpayne@68 164 public boolean equals(ReadKey b){
jpayne@68 165 return equals(b, false);
jpayne@68 166 }
jpayne@68 167
jpayne@68 168 @Override
jpayne@68 169 public String toString(){
jpayne@68 170 return position+","+(kmerMinusStrand ? ",t" : ",f")+","+kmer+"\t"+lane+","+tile+","+x+","+y;
jpayne@68 171 }
jpayne@68 172
jpayne@68 173 public float distance(ReadKey rkb){
jpayne@68 174 if(lane!=rkb.lane){return FlowcellCoordinate.big;}
jpayne@68 175
jpayne@68 176 long a=Tools.absdif(x, rkb.x), b=Tools.absdif(y, rkb.y);
jpayne@68 177 if(tile!=rkb.tile){
jpayne@68 178 if(spanTiles()){
jpayne@68 179 if(spanAdjacentOnly && Tools.absdif(tile, rkb.tile)>1){return FlowcellCoordinate.big;}
jpayne@68 180 if(spanTilesX && spanTilesY){
jpayne@68 181 return Tools.min(a, b);
jpayne@68 182 }else if(spanTilesX){
jpayne@68 183 return a;
jpayne@68 184 }else{
jpayne@68 185 return b;
jpayne@68 186 }
jpayne@68 187 }else{
jpayne@68 188 return FlowcellCoordinate.big;
jpayne@68 189 }
jpayne@68 190 }
jpayne@68 191 return (float)Math.sqrt(a*a+b*b);
jpayne@68 192 }
jpayne@68 193
jpayne@68 194 public boolean near(ReadKey rkb, float dist){
jpayne@68 195 return distance(rkb)<dist;
jpayne@68 196 }
jpayne@68 197
jpayne@68 198 public boolean nearXY(ReadKey rkb, float dist){
jpayne@68 199 if(lane!=rkb.lane){return false;}
jpayne@68 200
jpayne@68 201 long a=Tools.absdif(x, rkb.x), b=Tools.absdif(y, rkb.y);
jpayne@68 202 return Tools.min(a,b)<=dist;
jpayne@68 203 }
jpayne@68 204
jpayne@68 205 public int flag;
jpayne@68 206
jpayne@68 207 public long kmer;
jpayne@68 208 /** Position of rightmost base of kmer */
jpayne@68 209 public int position;
jpayne@68 210 public boolean flipped;
jpayne@68 211 public boolean kmerMinusStrand;
jpayne@68 212 public Clump clump;
jpayne@68 213 public IntList vars;
jpayne@68 214 // public float expectedErrors;
jpayne@68 215
jpayne@68 216 public int lane, tile, x, y;
jpayne@68 217
jpayne@68 218 public static final int overhead=overhead();
jpayne@68 219 private static int overhead(){
jpayne@68 220 return 16+ //self
jpayne@68 221 1*(8)+ //kmer
jpayne@68 222 1*(4)+ //int fields
jpayne@68 223 2*(4)+ //booleans
jpayne@68 224 2*(8)+ //pointers
jpayne@68 225 4*(4); //flowcell coordinate
jpayne@68 226 }
jpayne@68 227
jpayne@68 228 public static boolean spanTiles(){return spanTilesX || spanTilesY;}
jpayne@68 229 public static boolean spanTilesX=false;
jpayne@68 230 public static boolean spanTilesY=false;
jpayne@68 231 public static boolean spanAdjacentOnly=false;
jpayne@68 232
jpayne@68 233 /**
jpayne@68 234 *
jpayne@68 235 */
jpayne@68 236 private static final long serialVersionUID = 1L;
jpayne@68 237
jpayne@68 238 }