Mercurial > repos > rliterman > csp2

annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/bloom/KmerCount5.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 bloom;
jpayne@68 2
jpayne@68 3 import java.util.ArrayList;
jpayne@68 4 import java.util.BitSet;
jpayne@68 5 import java.util.Locale;
jpayne@68 6
jpayne@68 7 import dna.AminoAcid;
jpayne@68 8 import fileIO.FileFormat;
jpayne@68 9 import shared.Timer;
jpayne@68 10 import stream.ConcurrentReadInputStream;
jpayne@68 11 import stream.FastaReadInputStream;
jpayne@68 12 import stream.Read;
jpayne@68 13 import structures.ListNum;
jpayne@68 14
jpayne@68 15 /**
jpayne@68 16 * @author Brian Bushnell
jpayne@68 17 * @date Jul 5, 2012
jpayne@68 18 *
jpayne@68 19 */
jpayne@68 20 public class KmerCount5 extends KmerCountAbstract {
jpayne@68 21
jpayne@68 22 public static void main(String[] args){
jpayne@68 23
jpayne@68 24 Timer t=new Timer();
jpayne@68 25
jpayne@68 26 String fname1=args[0];
jpayne@68 27 String fname2=(args.length>1 ? args[1] : null);
jpayne@68 28 int k=14;
jpayne@68 29 int cbits=16;
jpayne@68 30 int gap=0;
jpayne@68 31
jpayne@68 32 for(int i=2; i<args.length; i++){
jpayne@68 33 final String arg=args[i];
jpayne@68 34 final String[] split=arg.split("=");
jpayne@68 35 String a=split[0].toLowerCase();
jpayne@68 36 String b=split.length>1 ? split[1] : null;
jpayne@68 37
jpayne@68 38 if(a.equals("k") || a.equals("kmer")){
jpayne@68 39 k=Integer.parseInt(b);
jpayne@68 40 }else if(a.startsWith("cbits") || a.startsWith("cellbits")){
jpayne@68 41 cbits=Integer.parseInt(b);
jpayne@68 42 }else if(a.startsWith("gap")){
jpayne@68 43 gap=Integer.parseInt(b);
jpayne@68 44 }else{
jpayne@68 45 throw new RuntimeException("Unknown parameter "+args[i]);
jpayne@68 46 }
jpayne@68 47 }
jpayne@68 48
jpayne@68 49 KCountArray count=null;
jpayne@68 50
jpayne@68 51 if(fileIO.FileFormat.hasFastaExtension(fname1)){
jpayne@68 52 assert(!FastaReadInputStream.SPLIT_READS);
jpayne@68 53 FastaReadInputStream.MIN_READ_LEN=k;
jpayne@68 54 }
jpayne@68 55
jpayne@68 56 if(gap==0){
jpayne@68 57 count=count(fname1, fname2, k, cbits, true);
jpayne@68 58 }else{
jpayne@68 59 count=countFastqSplit(fname1, fname2, (k+1)/2, k/2, gap, cbits, true, null);
jpayne@68 60 }
jpayne@68 61
jpayne@68 62
jpayne@68 63 t.stop();
jpayne@68 64 System.out.println("Finished counting; time = "+t);
jpayne@68 65
jpayne@68 66 printStatistics(count);
jpayne@68 67
jpayne@68 68 }
jpayne@68 69
jpayne@68 70 public static void printStatistics(KCountArray count){
jpayne@68 71 long[] freq=count.transformToFrequency();
jpayne@68 72
jpayne@68 73 // System.out.println(count+"\n");
jpayne@68 74 // System.out.println(Arrays.toString(freq)+"\n");
jpayne@68 75
jpayne@68 76 long sum=sum(freq);
jpayne@68 77 System.out.println("Kmer fraction:");
jpayne@68 78 int lim1=8, lim2=16;
jpayne@68 79 for(int i=0; i<lim1; i++){
jpayne@68 80 String prefix=i+"";
jpayne@68 81 while(prefix.length()<8){prefix=prefix+" ";}
jpayne@68 82 System.out.println(prefix+"\t"+String.format(Locale.ROOT, "%.3f%% ",(100l*freq[i]/(double)sum))+"\t"+freq[i]);
jpayne@68 83 }
jpayne@68 84 while(lim1<=freq.length){
jpayne@68 85 int x=0;
jpayne@68 86 for(int i=lim1; i<lim2; i++){
jpayne@68 87 x+=freq[i];
jpayne@68 88 }
jpayne@68 89 String prefix=lim1+"-"+(lim2-1);
jpayne@68 90 if(lim2>=freq.length){prefix=lim1+"+";}
jpayne@68 91 while(prefix.length()<8){prefix=prefix+" ";}
jpayne@68 92 System.out.println(prefix+"\t"+String.format(Locale.ROOT, "%.3f%% ",(100l*x/(double)sum))+"\t"+x);
jpayne@68 93 lim1*=2;
jpayne@68 94 lim2=min(lim2*2, freq.length);
jpayne@68 95 }
jpayne@68 96
jpayne@68 97 long sum2=sum-freq[0];
jpayne@68 98 long x=freq[1];
jpayne@68 99 System.out.println();
jpayne@68 100 System.out.println("Keys Counted: \t \t"+keysCounted);
jpayne@68 101 System.out.println("Unique: \t \t"+sum2);
jpayne@68 102 System.out.println("Avg Sites/Key: \t \t"+String.format(Locale.ROOT, "%.3f ",(keysCounted*1d/sum2)));
jpayne@68 103 System.out.println();
jpayne@68 104 System.out.println("Singleton: \t"+String.format(Locale.ROOT, "%.3f%% ",(100l*x/(double)sum2))+"\t"+x);
jpayne@68 105 x=sum2-x;
jpayne@68 106 System.out.println("Useful: \t"+String.format(Locale.ROOT, "%.3f%% ",(100l*x/(double)sum2))+"\t"+x);
jpayne@68 107 }
jpayne@68 108
jpayne@68 109 public static KCountArray count(String reads1, String reads2, int k, int cbits, boolean rcomp){
jpayne@68 110 return count(reads1, reads2, k, cbits, rcomp, null);
jpayne@68 111 }
jpayne@68 112
jpayne@68 113 public static KCountArray count(String reads1, String reads2, int k, int cbits, boolean rcomp, KCountArray count){
jpayne@68 114 assert(k<32 && k>=1 && (count!=null || k<20));
jpayne@68 115 final int kbits=2*k;
jpayne@68 116 final long mask=(kbits>63 ? -1L : ~((-1L)<<kbits));
jpayne@68 117
jpayne@68 118 if(count==null){
jpayne@68 119 final long cells=1L<<kbits;
jpayne@68 120 if(verbose){System.err.println("k="+k+", kbits="+kbits+", cells="+cells+", mask="+Long.toHexString(mask));}
jpayne@68 121 count=KCountArray.makeNew(cells, cbits);
jpayne@68 122 }
jpayne@68 123
jpayne@68 124 final ConcurrentReadInputStream cris;
jpayne@68 125 {
jpayne@68 126 FileFormat ff1=FileFormat.testInput(reads1, FileFormat.FASTQ, null, true, true);
jpayne@68 127 FileFormat ff2=FileFormat.testInput(reads2, FileFormat.FASTQ, null, true, true);
jpayne@68 128 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ff1, ff2);
jpayne@68 129 cris.start(); //4567
jpayne@68 130 }
jpayne@68 131
jpayne@68 132 assert(cris!=null) : reads1;
jpayne@68 133 System.err.println("Started cris");
jpayne@68 134 boolean paired=cris.paired();
jpayne@68 135 if(verbose){System.err.println("Paired: "+paired);}
jpayne@68 136
jpayne@68 137 ListNum<Read> ln=cris.nextList();
jpayne@68 138 ArrayList<Read> reads=(ln!=null ? ln.list : null);
jpayne@68 139
jpayne@68 140 if(reads!=null && !reads.isEmpty()){
jpayne@68 141 Read r=reads.get(0);
jpayne@68 142 assert(paired==(r.mate!=null));
jpayne@68 143 }
jpayne@68 144
jpayne@68 145 while(ln!=null && reads!=null && reads.size()>0){//ln!=null prevents a compiler potential null access warning
jpayne@68 146 //System.err.println("reads.size()="+reads.size());
jpayne@68 147 for(Read r : reads){
jpayne@68 148 readsProcessed++;
jpayne@68 149
jpayne@68 150 addRead(r, count, k, mask, rcomp);
jpayne@68 151 if(r.mate!=null){
jpayne@68 152 addRead(r.mate, count, k, mask, rcomp);
jpayne@68 153 }
jpayne@68 154
jpayne@68 155 }
jpayne@68 156 //System.err.println("returning list");
jpayne@68 157 cris.returnList(ln);
jpayne@68 158 //System.err.println("fetching list");
jpayne@68 159 ln=cris.nextList();
jpayne@68 160 reads=(ln!=null ? ln.list : null);
jpayne@68 161 }
jpayne@68 162 if(verbose){System.err.println("Finished reading");}
jpayne@68 163 cris.returnList(ln);
jpayne@68 164 if(verbose){System.err.println("Returned list");}
jpayne@68 165 cris.close();
jpayne@68 166 if(verbose){System.err.println("Closed stream");}
jpayne@68 167 if(verbose){System.err.println("Processed "+readsProcessed+" reads.");}
jpayne@68 168
jpayne@68 169
jpayne@68 170 return count;
jpayne@68 171 }
jpayne@68 172
jpayne@68 173
jpayne@68 174
jpayne@68 175
jpayne@68 176 public static KCountArray count(final String reads1, final String reads2, final int k, final int cbits, final boolean rcomp,
jpayne@68 177 KCountArray counts, final KCountArray trusted, final long maxReads, final int thresh, final int detectStepsize, final boolean conservative){
jpayne@68 178
jpayne@68 179 assert(k<32 && k>=1 && (counts!=null || k<20));
jpayne@68 180 final int kbits=2*k;
jpayne@68 181 final long mask=(kbits>63 ? -1L : ~((-1L)<<kbits));
jpayne@68 182
jpayne@68 183 // System.out.println("k="+k+", kbits="+kbits+", mask="+Long.toHexString(mask)+", thresh="+thresh);
jpayne@68 184 // System.out.println("\ntrusted=\n"+trusted);
jpayne@68 185 // System.out.println("\ncount=\n"+count);
jpayne@68 186
jpayne@68 187 if(counts==null){
jpayne@68 188 final long cells=1L<<kbits;
jpayne@68 189 if(verbose){System.err.println("k="+k+", kbits="+kbits+", cells="+cells+", mask="+Long.toHexString(mask));}
jpayne@68 190 counts=KCountArray.makeNew(cells, cbits);
jpayne@68 191 }
jpayne@68 192
jpayne@68 193 final ConcurrentReadInputStream cris;
jpayne@68 194 {
jpayne@68 195 FileFormat ff1=FileFormat.testInput(reads1, FileFormat.FASTQ, null, true, true);
jpayne@68 196 FileFormat ff2=FileFormat.testInput(reads2, FileFormat.FASTQ, null, true, true);
jpayne@68 197 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ff1, ff2);
jpayne@68 198 cris.start(); //4567
jpayne@68 199 }
jpayne@68 200
jpayne@68 201 assert(cris!=null) : reads1;
jpayne@68 202 System.err.println("Started cris");
jpayne@68 203 boolean paired=cris.paired();
jpayne@68 204 if(verbose){System.err.println("Paired: "+paired);}
jpayne@68 205
jpayne@68 206 ListNum<Read> ln=cris.nextList();
jpayne@68 207 ArrayList<Read> reads=(ln!=null ? ln.list : null);
jpayne@68 208
jpayne@68 209 if(reads!=null && !reads.isEmpty()){
jpayne@68 210 Read r=reads.get(0);
jpayne@68 211 assert(paired==(r.mate!=null));
jpayne@68 212 }
jpayne@68 213
jpayne@68 214
jpayne@68 215 while(ln!=null && reads!=null && reads.size()>0){//ln!=null prevents a compiler potential null access warning
jpayne@68 216 //System.err.println("reads.size()="+reads.size());
jpayne@68 217 for(Read r : reads){
jpayne@68 218
jpayne@68 219 Read r2=r.mate;
jpayne@68 220 {
jpayne@68 221 if(trusted!=null){
jpayne@68 222 BitSet bs=(conservative ? ErrorCorrect.detectErrorsBulk(r, trusted, k, thresh, detectStepsize) :
jpayne@68 223 ErrorCorrect.detectTrusted(r, trusted, k, thresh, detectStepsize));
jpayne@68 224 // System.out.println("\n"+toString(bs, r.length()));
jpayne@68 225 // System.out.println(new String(r.bases));
jpayne@68 226 for(int i=bs.nextClearBit(0); i<r.length(); i=bs.nextClearBit(i+1)){
jpayne@68 227 r.bases[i]='N';
jpayne@68 228 r.quality[i]=0;
jpayne@68 229 }
jpayne@68 230 // System.out.println(new String(r.bases));
jpayne@68 231 // System.out.println("used = "+String.format(Locale.ROOT, "%.3f%%",count.usedFraction()*100));
jpayne@68 232 // System.out.println("used = "+((KCountArray4)count).cellsUsed());
jpayne@68 233 // if(bs.length()<r.length()){r=null;}
jpayne@68 234 }
jpayne@68 235 // if(r!=null){KmerCount5.addRead(r, count, k, mask, rcomp);}
jpayne@68 236 KmerCount5.addRead(r, counts, k, mask, rcomp);
jpayne@68 237 }
jpayne@68 238 if(r2!=null){
jpayne@68 239 if(trusted!=null){
jpayne@68 240 BitSet bs=(conservative ? ErrorCorrect.detectErrorsBulk(r2, trusted, k, thresh, detectStepsize) :
jpayne@68 241 ErrorCorrect.detectTrusted(r2, trusted, k, thresh, detectStepsize));
jpayne@68 242 for(int i=bs.nextClearBit(0); i<r2.length(); i=bs.nextClearBit(i+1)){
jpayne@68 243 r2.bases[i]='N';
jpayne@68 244 r2.quality[i]=0;
jpayne@68 245 }
jpayne@68 246 }
jpayne@68 247 KmerCount5.addRead(r2, counts, k, mask, rcomp);
jpayne@68 248 }
jpayne@68 249
jpayne@68 250 }
jpayne@68 251 //System.err.println("returning list");
jpayne@68 252 cris.returnList(ln);
jpayne@68 253 //System.err.println("fetching list");
jpayne@68 254 ln=cris.nextList();
jpayne@68 255 reads=(ln!=null ? ln.list : null);
jpayne@68 256 }
jpayne@68 257
jpayne@68 258 if(verbose){System.err.println("Finished reading");}
jpayne@68 259 cris.returnList(ln);
jpayne@68 260 if(verbose){System.err.println("Returned list");}
jpayne@68 261 cris.close();
jpayne@68 262 if(verbose){System.err.println("Closed stream");}
jpayne@68 263
jpayne@68 264 // System.out.println("*** after ***");
jpayne@68 265 // System.out.println("\ntrusted=\n"+trusted);
jpayne@68 266 // System.out.println("\ncount=\n"+count);
jpayne@68 267
jpayne@68 268 return counts;
jpayne@68 269 }
jpayne@68 270
jpayne@68 271
jpayne@68 272 public static KCountArray countFastqSplit(String reads1, String reads2, int k1, int k2, int gap, int cbits, boolean rcomp, KCountArray counts){
jpayne@68 273 int k=k1+k2;
jpayne@68 274 assert(k<32 && k>=1 && (counts!=null || k<20));
jpayne@68 275 assert(gap>=0);
jpayne@68 276 final int kbits1=2*k1;
jpayne@68 277 final int kbits2=2*k2;
jpayne@68 278 final long mask1=~((-1L)<<(kbits1));
jpayne@68 279 final long mask2=~((-1L)<<(kbits2));
jpayne@68 280
jpayne@68 281 if(counts==null){
jpayne@68 282 final long cells=1L<<(kbits1+kbits2);
jpayne@68 283 if(verbose){System.err.println("k1="+k1+", k2="+k2+", kbits1="+kbits1+", kbits2="+kbits2+", cells="+cells+
jpayne@68 284 ", mask1="+Long.toHexString(mask1)+", mask2="+Long.toHexString(mask2));}
jpayne@68 285 counts=KCountArray.makeNew(cells, cbits);
jpayne@68 286 }
jpayne@68 287
jpayne@68 288 final ConcurrentReadInputStream cris;
jpayne@68 289 {
jpayne@68 290 FileFormat ff1=FileFormat.testInput(reads1, FileFormat.FASTQ, null, true, true);
jpayne@68 291 FileFormat ff2=FileFormat.testInput(reads2, FileFormat.FASTQ, null, true, true);
jpayne@68 292 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ff1, ff2);
jpayne@68 293 cris.start(); //4567
jpayne@68 294 }
jpayne@68 295
jpayne@68 296 assert(cris!=null) : reads1;
jpayne@68 297 System.err.println("Started cris");
jpayne@68 298 boolean paired=cris.paired();
jpayne@68 299 if(verbose){System.err.println("Paired: "+paired);}
jpayne@68 300
jpayne@68 301 ListNum<Read> ln=cris.nextList();
jpayne@68 302 ArrayList<Read> reads=(ln!=null ? ln.list : null);
jpayne@68 303
jpayne@68 304 if(reads!=null && !reads.isEmpty()){
jpayne@68 305 Read r=reads.get(0);
jpayne@68 306 assert(paired==(r.mate!=null));
jpayne@68 307 }
jpayne@68 308
jpayne@68 309 while(ln!=null && reads!=null && reads.size()>0){//ln!=null prevents a compiler potential null access warning
jpayne@68 310 //System.err.println("reads.size()="+reads.size());
jpayne@68 311 for(Read r : reads){
jpayne@68 312 readsProcessed++;
jpayne@68 313
jpayne@68 314 addReadSplit(r, counts, k1, k2, mask1, mask2, gap, rcomp);
jpayne@68 315 if(r.mate!=null){
jpayne@68 316 addReadSplit(r.mate, counts, k1, k2, mask1, mask2, gap, rcomp);
jpayne@68 317 }
jpayne@68 318
jpayne@68 319 }
jpayne@68 320 //System.err.println("returning list");
jpayne@68 321 cris.returnList(ln);
jpayne@68 322 //System.err.println("fetching list");
jpayne@68 323 ln=cris.nextList();
jpayne@68 324 reads=(ln!=null ? ln.list : null);
jpayne@68 325 }
jpayne@68 326 if(verbose){System.err.println("Finished reading");}
jpayne@68 327 cris.returnList(ln);
jpayne@68 328 if(verbose){System.err.println("Returned list");}
jpayne@68 329 cris.close();
jpayne@68 330 if(verbose){System.err.println("Closed stream");}
jpayne@68 331 if(verbose){System.err.println("Processed "+readsProcessed+" reads.");}
jpayne@68 332
jpayne@68 333
jpayne@68 334 return counts;
jpayne@68 335 }
jpayne@68 336
jpayne@68 337 public static void addRead(final Read r, final KCountArray count, final int k, final long mask, boolean rcomp){
jpayne@68 338 int len=0;
jpayne@68 339 long kmer=0;
jpayne@68 340 byte[] bases=r.bases;
jpayne@68 341 byte[] quals=r.quality;
jpayne@68 342 for(int i=0; i<bases.length; i++){
jpayne@68 343 byte b=bases[i];
jpayne@68 344 int x=AminoAcid.baseToNumber[b];
jpayne@68 345 if(x<0 || (quals!=null && quals[i]<minQuality)){
jpayne@68 346 len=0;
jpayne@68 347 kmer=0;
jpayne@68 348 }else{
jpayne@68 349 kmer=((kmer<<2)|x)&mask;
jpayne@68 350 len++;
jpayne@68 351 if(len>=k){
jpayne@68 352 keysCounted++;
jpayne@68 353 // System.out.print("Incrementing "+Long.toHexString(kmer)+": "+count.read(kmer));
jpayne@68 354 count.increment(kmer);
jpayne@68 355 // System.out.println(" -> "+count.read(kmer));
jpayne@68 356 // System.out.print("Incrementing array for "+Long.toHexString(kmer)+": "+array[(int)kmer]);
jpayne@68 357 // array[(int)kmer]++;
jpayne@68 358 // System.out.println(" -> "+array[(int)kmer]+"\n");
jpayne@68 359 // assert(array[(int)kmer]==count.read(kmer) || array[(int)kmer]>3);
jpayne@68 360 }
jpayne@68 361 }
jpayne@68 362 }
jpayne@68 363 if(rcomp){
jpayne@68 364 r.reverseComplement();
jpayne@68 365 addRead(r, count, k, mask, false);
jpayne@68 366 }
jpayne@68 367 }
jpayne@68 368
jpayne@68 369 public static void addReadSplit(final Read r, final KCountArray count, final int k1, final int k2, final long mask1, final long mask2, final int gap, boolean rcomp){
jpayne@68 370 int len=0;
jpayne@68 371 int shift=k2*2;
jpayne@68 372 long kmer1=0;
jpayne@68 373 long kmer2=0;
jpayne@68 374 byte[] bases=r.bases;
jpayne@68 375 byte[] quals=r.quality;
jpayne@68 376
jpayne@68 377 assert(kmer1>=kmer2);
jpayne@68 378
jpayne@68 379 // assert(false) : k1+", "+k2+", "+mask1+", "+mask2+", "+gap;
jpayne@68 380
jpayne@68 381 for(int i=0, j=i+k1+gap; j<bases.length; i++, j++){
jpayne@68 382 int x1=AminoAcid.baseToNumber[bases[i]];
jpayne@68 383 int x2=AminoAcid.baseToNumber[bases[j]];
jpayne@68 384 if(x1<0 || x2<0 || (quals!=null && (quals[i]<minQuality || quals[j]<minQuality))){
jpayne@68 385 len=0;
jpayne@68 386 kmer1=0;
jpayne@68 387 kmer2=0;
jpayne@68 388 }else{
jpayne@68 389 kmer1=((kmer1<<2)|x1)&mask1;
jpayne@68 390 kmer2=((kmer2<<2)|x2)&mask2;
jpayne@68 391 len++;
jpayne@68 392 if(len>=k1){
jpayne@68 393 keysCounted++;
jpayne@68 394 // System.out.print("Incrementing "+Long.toHexString(kmer)+": "+count.read(kmer));
jpayne@68 395
jpayne@68 396 long key=(kmer1<<shift)|kmer2;
jpayne@68 397 // System.err.println(Long.toHexString(key));
jpayne@68 398 count.increment(key);
jpayne@68 399 // System.out.println(" -> "+count.read(kmer));
jpayne@68 400 // System.out.print("Incrementing array for "+Long.toHexString(kmer)+": "+array[(int)kmer]);
jpayne@68 401 // array[(int)kmer]++;
jpayne@68 402 // System.out.println(" -> "+array[(int)kmer]+"\n");
jpayne@68 403 // assert(array[(int)kmer]==count.read(kmer) || array[(int)kmer]>3);
jpayne@68 404 }
jpayne@68 405 }
jpayne@68 406 }
jpayne@68 407 if(rcomp){
jpayne@68 408 r.reverseComplement();
jpayne@68 409 addReadSplit(r, count, k1, k2, mask1, mask2, gap, false);
jpayne@68 410 }
jpayne@68 411 }
jpayne@68 412
jpayne@68 413 public static void addReadSplit(final byte[] bases, final KCountArray count, final int k1, final int k2, final long mask1, final long mask2, final int gap, boolean rcomp){
jpayne@68 414 int len=0;
jpayne@68 415 int shift=k2*2;
jpayne@68 416 long kmer1=0;
jpayne@68 417 long kmer2=0;
jpayne@68 418 byte[] quals=null;
jpayne@68 419
jpayne@68 420 assert(kmer1>=kmer2);
jpayne@68 421
jpayne@68 422 // assert(false) : k1+", "+k2+", "+mask1+", "+mask2+", "+gap;
jpayne@68 423
jpayne@68 424 for(int i=0, j=i+k1+gap; j<bases.length; i++, j++){
jpayne@68 425 int x1=AminoAcid.baseToNumber[bases[i]];
jpayne@68 426 int x2=AminoAcid.baseToNumber[bases[j]];
jpayne@68 427 if(x1<0 || x2<0 || (quals!=null && (quals[i]<minQuality || quals[j]<minQuality))){
jpayne@68 428 len=0;
jpayne@68 429 kmer1=0;
jpayne@68 430 kmer2=0;
jpayne@68 431 }else{
jpayne@68 432 kmer1=((kmer1<<2)|x1)&mask1;
jpayne@68 433 kmer2=((kmer2<<2)|x2)&mask2;
jpayne@68 434 len++;
jpayne@68 435 if(len>=k1){
jpayne@68 436 keysCounted++;
jpayne@68 437 // System.out.print("Incrementing "+Long.toHexString(kmer)+": "+count.read(kmer));
jpayne@68 438
jpayne@68 439 long key=(kmer1<<shift)|kmer2;
jpayne@68 440 System.out.println(Long.toHexString(kmer1));
jpayne@68 441 System.out.println(Long.toHexString(kmer2));
jpayne@68 442 System.out.println(Long.toHexString(key));
jpayne@68 443 count.increment(key);
jpayne@68 444 // System.out.println(" -> "+count.read(kmer));
jpayne@68 445 // System.out.print("Incrementing array for "+Long.toHexString(kmer)+": "+array[(int)kmer]);
jpayne@68 446 // array[(int)kmer]++;
jpayne@68 447 // System.out.println(" -> "+array[(int)kmer]+"\n");
jpayne@68 448 // assert(array[(int)kmer]==count.read(kmer) || array[(int)kmer]>3);
jpayne@68 449 }
jpayne@68 450 }
jpayne@68 451 }
jpayne@68 452 if(rcomp){
jpayne@68 453 AminoAcid.reverseComplementBasesInPlace(bases);
jpayne@68 454 addReadSplit(bases, count, k1, k2, mask1, mask2, gap, false);
jpayne@68 455 }
jpayne@68 456 }
jpayne@68 457
jpayne@68 458 }