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annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/sketch/KmerLimit2.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 sketch;
jpayne@68 2
jpayne@68 3 import java.io.File;
jpayne@68 4 import java.io.PrintStream;
jpayne@68 5 import java.util.ArrayList;
jpayne@68 6 import java.util.Arrays;
jpayne@68 7 import java.util.Locale;
jpayne@68 8 import java.util.Random;
jpayne@68 9
jpayne@68 10 import dna.AminoAcid;
jpayne@68 11 import fileIO.ByteFile;
jpayne@68 12 import fileIO.FileFormat;
jpayne@68 13 import fileIO.ReadWrite;
jpayne@68 14 import shared.Parse;
jpayne@68 15 import shared.Parser;
jpayne@68 16 import shared.PreParser;
jpayne@68 17 import shared.ReadStats;
jpayne@68 18 import shared.Shared;
jpayne@68 19 import shared.Timer;
jpayne@68 20 import shared.Tools;
jpayne@68 21 import stream.ConcurrentReadInputStream;
jpayne@68 22 import stream.ConcurrentReadOutputStream;
jpayne@68 23 import stream.FASTQ;
jpayne@68 24 import stream.FastaReadInputStream;
jpayne@68 25 import stream.Read;
jpayne@68 26 import structures.IntMap;
jpayne@68 27 import structures.ListNum;
jpayne@68 28
jpayne@68 29 /**
jpayne@68 30 *
jpayne@68 31 * @author Brian Bushnell
jpayne@68 32 * @date July 30, 2018
jpayne@68 33 *
jpayne@68 34 */
jpayne@68 35 public class KmerLimit2 extends SketchObject {
jpayne@68 36
jpayne@68 37 /*--------------------------------------------------------------*/
jpayne@68 38 /*---------------- Initialization ----------------*/
jpayne@68 39 /*--------------------------------------------------------------*/
jpayne@68 40
jpayne@68 41 /**
jpayne@68 42 * Code entrance from the command line.
jpayne@68 43 * @param args Command line arguments
jpayne@68 44 */
jpayne@68 45 public static void main(String[] args){
jpayne@68 46 //Start a timer immediately upon code entrance.
jpayne@68 47 Timer t=new Timer();
jpayne@68 48
jpayne@68 49 //Create an instance of this class
jpayne@68 50 KmerLimit2 x=new KmerLimit2(args);
jpayne@68 51
jpayne@68 52 //Run the object
jpayne@68 53 x.process(t);
jpayne@68 54
jpayne@68 55 //Close the print stream if it was redirected
jpayne@68 56 Shared.closeStream(x.outstream);
jpayne@68 57 }
jpayne@68 58
jpayne@68 59 /**
jpayne@68 60 * Constructor.
jpayne@68 61 * @param args Command line arguments
jpayne@68 62 */
jpayne@68 63 public KmerLimit2(String[] args){
jpayne@68 64
jpayne@68 65 {//Preparse block for help, config files, and outstream
jpayne@68 66 PreParser pp=new PreParser(args, getClass(), false);
jpayne@68 67 args=pp.args;
jpayne@68 68 outstream=pp.outstream;
jpayne@68 69 }
jpayne@68 70
jpayne@68 71 boolean setInterleaved=false; //Whether interleaved was explicitly set.
jpayne@68 72
jpayne@68 73 //Set shared static variables
jpayne@68 74 ReadWrite.USE_PIGZ=ReadWrite.USE_UNPIGZ=true;
jpayne@68 75 ReadWrite.MAX_ZIP_THREADS=Shared.threads();
jpayne@68 76 SketchObject.setKeyFraction(0.1);
jpayne@68 77 defaultParams.minEntropy=0;
jpayne@68 78 defaultParams.minProb=0.2f;
jpayne@68 79
jpayne@68 80 boolean setHeapSize=false;
jpayne@68 81 int heapSize_=8091;
jpayne@68 82 long targetKmers_=0;
jpayne@68 83 int k_=32;
jpayne@68 84 int minCount_=1;
jpayne@68 85
jpayne@68 86 //Create a parser object
jpayne@68 87 Parser parser=new Parser();
jpayne@68 88 parser.overwrite=true;
jpayne@68 89
jpayne@68 90 //Parse each argument
jpayne@68 91 for(int i=0; i<args.length; i++){
jpayne@68 92 String arg=args[i];
jpayne@68 93
jpayne@68 94 //Break arguments into their constituent parts, in the form of "a=b"
jpayne@68 95 String[] split=arg.split("=");
jpayne@68 96 String a=split[0].toLowerCase();
jpayne@68 97 String b=split.length>1 ? split[1] : null;
jpayne@68 98 if(b!=null && b.equalsIgnoreCase("null")){b=null;}
jpayne@68 99
jpayne@68 100 if(a.equals("verbose")){
jpayne@68 101 verbose=Parse.parseBoolean(b);
jpayne@68 102 }else if(a.equals("ordered")){
jpayne@68 103 ordered=Parse.parseBoolean(b);
jpayne@68 104 }else if(a.equals("size") || a.equals("heapsize")){
jpayne@68 105 heapSize_=Parse.parseIntKMG(b);
jpayne@68 106 setHeapSize=true;
jpayne@68 107 }else if(a.equals("kmers") || a.equals("target") || a.equals("limit")){
jpayne@68 108 targetKmers_=Parse.parseKMG(b);
jpayne@68 109 }else if(a.equals("mincount")){
jpayne@68 110 minCount_=Parse.parseIntKMG(b);
jpayne@68 111 }else if(a.equals("maxexpandedlength") || a.equals("maxlength") || a.equals("maxlen")){
jpayne@68 112 maxExpandedLength=Parse.parseIntKMG(b);
jpayne@68 113 }else if(a.equals("seed")){
jpayne@68 114 seed=Parse.parseKMG(b);
jpayne@68 115 }else if(a.equals("trials")){
jpayne@68 116 trials=Parse.parseIntKMG(b);
jpayne@68 117 }else if(parseSketchFlags(arg, a, b)){
jpayne@68 118 parser.parse(arg, a, b);
jpayne@68 119 }else if(defaultParams.parse(arg, a, b)){
jpayne@68 120 parser.parse(arg, a, b);
jpayne@68 121 }else if(a.equals("parse_flag_goes_here")){
jpayne@68 122 long fake_variable=Parse.parseKMG(b);
jpayne@68 123 //Set a variable here
jpayne@68 124 }else if(parser.parse(arg, a, b)){//Parse standard flags in the parser
jpayne@68 125 //do nothing
jpayne@68 126 }else{
jpayne@68 127 outstream.println("Unknown parameter "+args[i]);
jpayne@68 128 assert(false) : "Unknown parameter "+args[i];
jpayne@68 129 }
jpayne@68 130 }
jpayne@68 131
jpayne@68 132 if(!setHeapSize && minCount_>1){heapSize_=32000;}
jpayne@68 133 heapSize=heapSize_;
jpayne@68 134 targetKmers=targetKmers_;
jpayne@68 135 k=k_;
jpayne@68 136 minCount=minCount_;
jpayne@68 137 assert(targetKmers>0) : "Must set a kmer limit.";
jpayne@68 138 assert(heapSize>0) : "Heap size must be positive.";
jpayne@68 139 assert(k>0 && k<=32) : "0<k<33; k="+k;
jpayne@68 140 postParse();
jpayne@68 141
jpayne@68 142 // if(minCount>1){
jpayne@68 143 // Shared.setBufferLen(800);
jpayne@68 144 // }
jpayne@68 145
jpayne@68 146 {//Process parser fields
jpayne@68 147 Parser.processQuality();
jpayne@68 148
jpayne@68 149 maxReads=parser.maxReads;
jpayne@68 150
jpayne@68 151 overwrite=ReadStats.overwrite=parser.overwrite;
jpayne@68 152 append=ReadStats.append=parser.append;
jpayne@68 153 setInterleaved=parser.setInterleaved;
jpayne@68 154
jpayne@68 155 in1=parser.in1;
jpayne@68 156 in2=parser.in2;
jpayne@68 157 qfin1=parser.qfin1;
jpayne@68 158 qfin2=parser.qfin2;
jpayne@68 159
jpayne@68 160 out1=parser.out1;
jpayne@68 161 out2=parser.out2;
jpayne@68 162 qfout1=parser.qfout1;
jpayne@68 163 qfout2=parser.qfout2;
jpayne@68 164
jpayne@68 165 extin=parser.extin;
jpayne@68 166 extout=parser.extout;
jpayne@68 167 }
jpayne@68 168
jpayne@68 169 //Do input file # replacement
jpayne@68 170 if(in1!=null && in2==null && in1.indexOf('#')>-1 && !new File(in1).exists()){
jpayne@68 171 in2=in1.replace("#", "2");
jpayne@68 172 in1=in1.replace("#", "1");
jpayne@68 173 }
jpayne@68 174
jpayne@68 175 //Do output file # replacement
jpayne@68 176 if(out1!=null && out2==null && out1.indexOf('#')>-1){
jpayne@68 177 out2=out1.replace("#", "2");
jpayne@68 178 out1=out1.replace("#", "1");
jpayne@68 179 }
jpayne@68 180
jpayne@68 181 //Adjust interleaved detection based on the number of input files
jpayne@68 182 if(in2!=null){
jpayne@68 183 if(FASTQ.FORCE_INTERLEAVED){outstream.println("Reset INTERLEAVED to false because paired input files were specified.");}
jpayne@68 184 FASTQ.FORCE_INTERLEAVED=FASTQ.TEST_INTERLEAVED=false;
jpayne@68 185 }
jpayne@68 186
jpayne@68 187 assert(FastaReadInputStream.settingsOK());
jpayne@68 188
jpayne@68 189 //Ensure there is an input file
jpayne@68 190 if(in1==null){throw new RuntimeException("Error - at least one input file is required.");}
jpayne@68 191
jpayne@68 192 //Adjust the number of threads for input file reading
jpayne@68 193 if(!ByteFile.FORCE_MODE_BF1 && !ByteFile.FORCE_MODE_BF2 && Shared.threads()>2){
jpayne@68 194 ByteFile.FORCE_MODE_BF2=true;
jpayne@68 195 }
jpayne@68 196
jpayne@68 197 //Ensure out2 is not set without out1
jpayne@68 198 if(out1==null && out2!=null){throw new RuntimeException("Error - cannot define out2 without defining out1.");}
jpayne@68 199
jpayne@68 200 //Adjust interleaved settings based on number of output files
jpayne@68 201 if(!setInterleaved){
jpayne@68 202 assert(in1!=null && (out1!=null || out2==null)) : "\nin1="+in1+"\nin2="+in2+"\nout1="+out1+"\nout2="+out2+"\n";
jpayne@68 203 if(in2!=null){ //If there are 2 input streams.
jpayne@68 204 FASTQ.FORCE_INTERLEAVED=FASTQ.TEST_INTERLEAVED=false;
jpayne@68 205 outstream.println("Set INTERLEAVED to "+FASTQ.FORCE_INTERLEAVED);
jpayne@68 206 }else{ //There is one input stream.
jpayne@68 207 if(out2!=null){
jpayne@68 208 FASTQ.FORCE_INTERLEAVED=true;
jpayne@68 209 FASTQ.TEST_INTERLEAVED=false;
jpayne@68 210 outstream.println("Set INTERLEAVED to "+FASTQ.FORCE_INTERLEAVED);
jpayne@68 211 }
jpayne@68 212 }
jpayne@68 213 }
jpayne@68 214
jpayne@68 215 //Ensure output files can be written
jpayne@68 216 if(!Tools.testOutputFiles(overwrite, append, false, out1, out2)){
jpayne@68 217 outstream.println((out1==null)+", "+(out2==null)+", "+out1+", "+out2);
jpayne@68 218 throw new RuntimeException("\n\noverwrite="+overwrite+"; Can't write to output files "+out1+", "+out2+"\n");
jpayne@68 219 }
jpayne@68 220
jpayne@68 221 //Ensure input files can be read
jpayne@68 222 if(!Tools.testInputFiles(false, true, in1, in2)){
jpayne@68 223 throw new RuntimeException("\nCan't read some input files.\n");
jpayne@68 224 }
jpayne@68 225
jpayne@68 226 //Ensure that no file was specified multiple times
jpayne@68 227 if(!Tools.testForDuplicateFiles(true, in1, in2, out1, out2)){
jpayne@68 228 throw new RuntimeException("\nSome file names were specified multiple times.\n");
jpayne@68 229 }
jpayne@68 230
jpayne@68 231 //Create output FileFormat objects
jpayne@68 232 ffout1=FileFormat.testOutput(out1, FileFormat.FASTQ, extout, true, overwrite, append, ordered);
jpayne@68 233 ffout2=FileFormat.testOutput(out2, FileFormat.FASTQ, extout, true, overwrite, append, ordered);
jpayne@68 234
jpayne@68 235 //Create input FileFormat objects
jpayne@68 236 ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, extin, true, true);
jpayne@68 237 ffin2=FileFormat.testInput(in2, FileFormat.FASTQ, extin, true, true);
jpayne@68 238
jpayne@68 239 minProb=defaultParams.minProb;
jpayne@68 240 minQual=defaultParams.minQual;
jpayne@68 241
jpayne@68 242 shift=2*k;
jpayne@68 243 shift2=shift-2;
jpayne@68 244 mask=(shift>63 ? -1L : ~((-1L)<<shift)); //Conditional allows K=32
jpayne@68 245 sharedHeap=new SketchHeap(heapSize, 0, true);
jpayne@68 246 }
jpayne@68 247
jpayne@68 248 /*--------------------------------------------------------------*/
jpayne@68 249 /*---------------- Outer Methods ----------------*/
jpayne@68 250 /*--------------------------------------------------------------*/
jpayne@68 251
jpayne@68 252 /** Create read streams and process all data */
jpayne@68 253 void process(Timer t){
jpayne@68 254
jpayne@68 255 //Turn off read validation in the input threads to increase speed
jpayne@68 256 final boolean vic=Read.VALIDATE_IN_CONSTRUCTOR;
jpayne@68 257 Read.VALIDATE_IN_CONSTRUCTOR=Shared.threads()<4;
jpayne@68 258
jpayne@68 259 // //Optionally create a read output stream
jpayne@68 260 // final ConcurrentReadOutputStream ros;
jpayne@68 261 // if(ffout1!=null){
jpayne@68 262 // //Select output buffer size based on whether it needs to be ordered
jpayne@68 263 // final int buff=(ordered ? Tools.mid(16, 128, (Shared.threads()*2)/3) : 8);
jpayne@68 264 //
jpayne@68 265 // //Notify user of output mode
jpayne@68 266 // if(cris.paired() && out2==null && (in1!=null && !ffin1.samOrBam() && !ffout1.samOrBam())){
jpayne@68 267 // outstream.println("Writing interleaved.");
jpayne@68 268 // }
jpayne@68 269 //
jpayne@68 270 // ros=ConcurrentReadOutputStream.getStream(ffout1, ffout2, qfout1, qfout2, buff, null, false);
jpayne@68 271 // ros.start(); //Start the stream
jpayne@68 272 // }else{ros=null;}
jpayne@68 273
jpayne@68 274 //Reset counters
jpayne@68 275 readsProcessed=readsOut=0;
jpayne@68 276 basesProcessed=basesOut=0;
jpayne@68 277
jpayne@68 278 //Process the reads in separate threads
jpayne@68 279 spawnThreads0();
jpayne@68 280
jpayne@68 281 // if(verbose){outstream.println("Finished; closing streams.");}
jpayne@68 282
jpayne@68 283 //Reset read validation
jpayne@68 284 Read.VALIDATE_IN_CONSTRUCTOR=vic;
jpayne@68 285
jpayne@68 286
jpayne@68 287 Sketch sketch=new Sketch(sharedHeap, true, true, null);
jpayne@68 288 sketch=capLengthAtCountSum(sketch, maxExpandedLength);
jpayne@68 289 final long reads=Tools.max(1, sketch.genomeSequences);
jpayne@68 290 final long targetReads=calcTargetReads(sketch, targetKmers, minCount, trials, seed);
jpayne@68 291 final double targetRate=Tools.min(1, targetReads/(double)reads);
jpayne@68 292 final String targetRateS=String.format(Locale.ROOT, "%.4f%%",targetRate*100);
jpayne@68 293
jpayne@68 294 //Report timing and results
jpayne@68 295 t.stop();
jpayne@68 296 outstream.println("Finished counting kmers.");
jpayne@68 297 outstream.println(Tools.timeReadsBasesProcessed(t, readsProcessed, basesProcessed, 8));
jpayne@68 298
jpayne@68 299 String kstring0=Tools.padKM(sketch.genomeSizeEstimate(minCount), 8);
jpayne@68 300 String rstring0=Tools.padKM(targetReads, 8);
jpayne@68 301 outstream.println("Unique Kmers: "+kstring0);
jpayne@68 302 outstream.println("Target Reads: "+rstring0+"\t"+targetRateS);
jpayne@68 303
jpayne@68 304 // outstream.println("Reads: \t"+reads);
jpayne@68 305 // outstream.println("Unique Kmers: \t"+sketch.genomeSizeEstimate(minCount));
jpayne@68 306 // outstream.println("Target Reads: \t"+targetReads);
jpayne@68 307 // outstream.println("Sample Rate: \t"+targetRateS);
jpayne@68 308 // outstream.println(Tools.readsBasesOut(readsProcessed, basesProcessed, readsOut, basesOut, 8, false));
jpayne@68 309
jpayne@68 310 t.start();
jpayne@68 311 outstream.println("\nSubsampling reads.");
jpayne@68 312
jpayne@68 313 // String kstring=Tools.padKM(sharedHeap.genomeSizeEstimate(minCount), 8);
jpayne@68 314 // outstream.println("Unique Kmers Out: "+kstring);
jpayne@68 315
jpayne@68 316
jpayne@68 317 // ArrayList<String> args=new ArrayList<String>();
jpayne@68 318 // args.add("in="+in1);
jpayne@68 319 // if(in2!=null){args.add("in2="+in2);}
jpayne@68 320 // args.add("out="+out1);
jpayne@68 321 // if(out2!=null){args.add("out2="+out2);}
jpayne@68 322 // args.add("ordered="+ordered);
jpayne@68 323 // args.add("ow="+(overwrite ? "t" : "f"));
jpayne@68 324 // if(targetRate<1){args.add("samplerate="+targetRateS);}
jpayne@68 325 // args.add("loglogout");
jpayne@68 326 // args.add("loglogk="+k);
jpayne@68 327 // args.add("loglogminprob="+minProb);
jpayne@68 328 // BBDukF.main(args.toArray(new String[0]));
jpayne@68 329
jpayne@68 330 // Sketch sk=new Sketch(sharedHeap, true, true, null);
jpayne@68 331 // outstream.println(sk.genomeSizeEstimate());
jpayne@68 332 spawnThreads2(targetRate);
jpayne@68 333 t.stop();
jpayne@68 334 outstream.println(Tools.timeReadsBasesProcessed(t, readsProcessed, basesProcessed, 8));
jpayne@68 335
jpayne@68 336 outstream.println(Tools.readsBasesOut(readsProcessed, basesProcessed, readsOut, basesOut, 8, false));
jpayne@68 337 String kstring=Tools.padKM(sharedHeap.genomeSizeEstimate(minCount), 8);
jpayne@68 338 outstream.println("Unique Kmers Out: "+kstring);
jpayne@68 339
jpayne@68 340 //Throw an exception of there was an error in a thread
jpayne@68 341 if(errorState){
jpayne@68 342 throw new RuntimeException(getClass().getName()+" terminated in an error state; the output may be corrupt.");
jpayne@68 343 }
jpayne@68 344 }
jpayne@68 345
jpayne@68 346 /** Spawn process threads */
jpayne@68 347 private void spawnThreads0(){
jpayne@68 348
jpayne@68 349 //Create a read input stream
jpayne@68 350 final ConcurrentReadInputStream cris;
jpayne@68 351 {
jpayne@68 352 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2);
jpayne@68 353 cris.start(); //Start the stream
jpayne@68 354 if(verbose){outstream.println("Started cris");}
jpayne@68 355 }
jpayne@68 356 paired=cris.paired();
jpayne@68 357 if(!ffin1.samOrBam()){outstream.println("Input is being processed as "+(paired ? "paired" : "unpaired"));}
jpayne@68 358
jpayne@68 359 //Determine how many threads may be used
jpayne@68 360 final int threads=Tools.min(10, Shared.threads());
jpayne@68 361
jpayne@68 362 //Fill a list with ProcessThreads
jpayne@68 363 ArrayList<ProcessThread> alpt=new ArrayList<ProcessThread>(threads);
jpayne@68 364 for(int i=0; i<threads; i++){
jpayne@68 365 alpt.add(new ProcessThread(cris, null, i, heapSize));
jpayne@68 366 }
jpayne@68 367
jpayne@68 368 //Start the threads
jpayne@68 369 for(ProcessThread pt : alpt){
jpayne@68 370 pt.start();
jpayne@68 371 }
jpayne@68 372
jpayne@68 373 //Wait for completion of all threads
jpayne@68 374 boolean success=true;
jpayne@68 375 for(ProcessThread pt : alpt){
jpayne@68 376
jpayne@68 377 //Wait until this thread has terminated
jpayne@68 378 while(pt.getState()!=Thread.State.TERMINATED){
jpayne@68 379 try {
jpayne@68 380 //Attempt a join operation
jpayne@68 381 pt.join();
jpayne@68 382 } catch (InterruptedException e) {
jpayne@68 383 //Potentially handle this, if it is expected to occur
jpayne@68 384 e.printStackTrace();
jpayne@68 385 }
jpayne@68 386 }
jpayne@68 387
jpayne@68 388 //Accumulate per-thread statistics
jpayne@68 389 readsProcessed+=pt.readsProcessedT;
jpayne@68 390 basesProcessed+=pt.basesProcessedT;
jpayne@68 391 readsOut+=pt.readsOutT;
jpayne@68 392 basesOut+=pt.basesOutT;
jpayne@68 393 success&=pt.success;
jpayne@68 394 }
jpayne@68 395
jpayne@68 396 //Track whether any threads failed
jpayne@68 397 if(!success){errorState=true;}
jpayne@68 398
jpayne@68 399 //Do anything necessary after processing
jpayne@68 400
jpayne@68 401 //Close the read streams
jpayne@68 402 errorState|=ReadWrite.closeStreams(cris);
jpayne@68 403
jpayne@68 404 }
jpayne@68 405
jpayne@68 406 /** Spawn process threads */
jpayne@68 407 private void spawnThreads2(double rate){
jpayne@68 408
jpayne@68 409 //Create a read input stream
jpayne@68 410 final ConcurrentReadInputStream cris;
jpayne@68 411 {
jpayne@68 412 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2);
jpayne@68 413 cris.setSampleRate((float)rate, seed);
jpayne@68 414 cris.start(); //Start the stream
jpayne@68 415 if(verbose){outstream.println("Started cris");}
jpayne@68 416 }
jpayne@68 417 // paired=cris.paired();
jpayne@68 418 // if(!ffin1.samOrBam()){outstream.println("Input is being processed as "+(paired ? "paired" : "unpaired"));}
jpayne@68 419
jpayne@68 420 //Optionally create a read output stream
jpayne@68 421 final ConcurrentReadOutputStream ros;
jpayne@68 422 if(ffout1!=null){
jpayne@68 423 //Select output buffer size based on whether it needs to be ordered
jpayne@68 424 final int buff=(ordered ? Tools.mid(16, 128, (Shared.threads()*2)/3) : 8);
jpayne@68 425
jpayne@68 426 //Notify user of output mode
jpayne@68 427 if(cris.paired() && out2==null && (in1!=null && !ffin1.samOrBam() && !ffout1.samOrBam())){
jpayne@68 428 outstream.println("Writing interleaved.");
jpayne@68 429 }
jpayne@68 430
jpayne@68 431 ros=ConcurrentReadOutputStream.getStream(ffout1, ffout2, qfout1, qfout2, buff, null, false);
jpayne@68 432 ros.start(); //Start the stream
jpayne@68 433 }else{ros=null;}
jpayne@68 434
jpayne@68 435 //Determine how many threads may be used
jpayne@68 436 final int threads=Tools.min(10, Shared.threads());
jpayne@68 437
jpayne@68 438 sharedHeap.clear();
jpayne@68 439 // readsProcessed=0;
jpayne@68 440 // basesProcessed=0;
jpayne@68 441 readsOut=0;
jpayne@68 442 basesOut=0;
jpayne@68 443
jpayne@68 444 //Fill a list with ProcessThreads
jpayne@68 445 ArrayList<ProcessThread> alpt=new ArrayList<ProcessThread>(threads);
jpayne@68 446 for(int i=0; i<threads; i++){
jpayne@68 447 alpt.add(new ProcessThread(cris, ros, i, heapSize));
jpayne@68 448 }
jpayne@68 449
jpayne@68 450 //Start the threads
jpayne@68 451 for(ProcessThread pt : alpt){
jpayne@68 452 pt.start();
jpayne@68 453 }
jpayne@68 454
jpayne@68 455 //Wait for completion of all threads
jpayne@68 456 boolean success=true;
jpayne@68 457 for(ProcessThread pt : alpt){
jpayne@68 458
jpayne@68 459 //Wait until this thread has terminated
jpayne@68 460 while(pt.getState()!=Thread.State.TERMINATED){
jpayne@68 461 try {
jpayne@68 462 //Attempt a join operation
jpayne@68 463 pt.join();
jpayne@68 464 } catch (InterruptedException e) {
jpayne@68 465 //Potentially handle this, if it is expected to occur
jpayne@68 466 e.printStackTrace();
jpayne@68 467 }
jpayne@68 468 }
jpayne@68 469
jpayne@68 470 //Accumulate per-thread statistics
jpayne@68 471 // readsProcessed+=pt.readsProcessedT;
jpayne@68 472 // basesProcessed+=pt.basesProcessedT;
jpayne@68 473 readsOut+=pt.readsOutT;
jpayne@68 474 basesOut+=pt.basesOutT;
jpayne@68 475 success&=pt.success;
jpayne@68 476 }
jpayne@68 477
jpayne@68 478 //Track whether any threads failed
jpayne@68 479 if(!success){errorState=true;}
jpayne@68 480
jpayne@68 481 //Do anything necessary after processing
jpayne@68 482
jpayne@68 483 //Write anything that was accumulated by ReadStats
jpayne@68 484 errorState|=ReadStats.writeAll();
jpayne@68 485 //Close the read streams
jpayne@68 486 errorState|=ReadWrite.closeStreams(cris, ros);
jpayne@68 487
jpayne@68 488 }
jpayne@68 489
jpayne@68 490 /*--------------------------------------------------------------*/
jpayne@68 491 /*---------------- Inner Methods ----------------*/
jpayne@68 492 /*--------------------------------------------------------------*/
jpayne@68 493
jpayne@68 494 public static Sketch capLengthAtCountSum(Sketch sketch0, int max) {
jpayne@68 495 int len=0;
jpayne@68 496 long sum=0;
jpayne@68 497 for(; len<sketch0.keyCounts.length; len++){
jpayne@68 498 sum=sum+sketch0.keyCounts[len];
jpayne@68 499 if(sum>max){break;}
jpayne@68 500 }
jpayne@68 501 if(len>=sketch0.length()){return sketch0;}
jpayne@68 502
jpayne@68 503 long[] keys=Arrays.copyOf(sketch0.keys, len);
jpayne@68 504 int[] counts=Arrays.copyOf(sketch0.keyCounts, len);
jpayne@68 505
jpayne@68 506 // long[] array_, int[] counts_, int taxID_, long imgID_, long gSizeBases_, long gSizeKmers_, long gSequences_, double probCorrect_,
jpayne@68 507 // String taxName_, String name0_, String fname_, ArrayList<String> meta_
jpayne@68 508
jpayne@68 509 Sketch sk=new Sketch(keys, counts, null, null, null, -1, -1,
jpayne@68 510 sketch0.genomeSizeBases, sketch0.genomeSizeKmers, sketch0.genomeSequences, sketch0.probCorrect,
jpayne@68 511 null, null, null, null);
jpayne@68 512
jpayne@68 513 return sk;
jpayne@68 514 }
jpayne@68 515
jpayne@68 516 public static long calcTargetReads(Sketch sketch, long targetKmers, int minCount, int trials, long seed){
jpayne@68 517 final int[] counts0=sketch.keyCounts;
jpayne@68 518 final int[] counts=Arrays.copyOf(counts0, counts0.length);
jpayne@68 519 final long size=sketch.genomeSizeEstimate(minCount);
jpayne@68 520 final long reads=sketch.genomeSequences;
jpayne@68 521 final double targetKmerFraction=targetKmers/(double)size;
jpayne@68 522 if(targetKmerFraction>=1){return reads;}
jpayne@68 523
jpayne@68 524 final int targetKeys=(int)(targetKmerFraction*counts.length);
jpayne@68 525 final long countSum=Tools.sum(counts0);
jpayne@68 526 assert(countSum<Shared.MAX_ARRAY_LEN) : countSum;
jpayne@68 527 // System.err.println("countsum: "+countSum);
jpayne@68 528
jpayne@68 529 final IntMap map=new IntMap(0, counts0.length);
jpayne@68 530 final int[] expanded=new int[(int)countSum];
jpayne@68 531
jpayne@68 532 long roundSum=0;
jpayne@68 533 final Random randy=Shared.threadLocalRandom(seed);
jpayne@68 534 for(int i=0; i<trials; i++){
jpayne@68 535 Tools.fill(counts, counts0);
jpayne@68 536 // long rounds=reduceRounds(counts0, counts, minCount, targetKeys, randy);
jpayne@68 537 long rounds=reduceRoundsIM(counts0, expanded, minCount, targetKeys, randy, map);
jpayne@68 538 roundSum+=rounds;
jpayne@68 539 }
jpayne@68 540 double avgRounds=roundSum/(double)trials;
jpayne@68 541 // System.err.println("avgRounds: "+avgRounds);
jpayne@68 542 double targetCountFraction=1-(avgRounds/countSum);
jpayne@68 543 // System.err.println("targetFraction: "+targetCountFraction);
jpayne@68 544 return (long)(targetCountFraction*reads);
jpayne@68 545 }
jpayne@68 546
jpayne@68 547 // public static int reduceRoundsOld(final int[] counts, final int minCount, final int targetKeys, final Random randy){
jpayne@68 548 // assert(minCount>=0) : minCount;
jpayne@68 549 // int rounds=0;
jpayne@68 550 // int valid=0;
jpayne@68 551 // for(int x : counts){
jpayne@68 552 // if(x>=minCount){valid++;}
jpayne@68 553 // }
jpayne@68 554 //
jpayne@68 555 // int len=counts.length;
jpayne@68 556 // System.err.println(targetKeys+", "+counts.length+", "+valid+", "+len+", "+rounds+", "+Tools.sum(counts)+", "+Arrays.toString(counts));
jpayne@68 557 // for(; valid>targetKeys; rounds++){
jpayne@68 558 // int pos=randy.nextInt(len);
jpayne@68 559 //// assert(counts[pos]>0) : pos+"/"+len+": "+targetKeys+", "+counts.length+", "+valid+", "+len+", "+rounds+", "+Arrays.toString(counts);
jpayne@68 560 // if(counts[pos]==minCount){valid--;}
jpayne@68 561 // counts[pos]--;
jpayne@68 562 // if(counts[pos]==0){
jpayne@68 563 // len--;//shrink the array
jpayne@68 564 // System.err.println("len="+len+", counts[len]="+counts[len]);
jpayne@68 565 // System.err.println("pos="+pos+", counts[pos]="+counts[pos]);
jpayne@68 566 // counts[pos]=counts[len];//move the last element to the empty slot
jpayne@68 567 // counts[len]=0;
jpayne@68 568 // if(pos!=len && len>0){
jpayne@68 569 // assert(counts[pos]>0) : pos+"/"+len+": "+targetKeys+", "+counts.length+", "+valid+", "+len+", "+rounds+", "+Arrays.toString(counts);
jpayne@68 570 // }
jpayne@68 571 // }
jpayne@68 572 // System.err.println(len+", "+pos+": "+Arrays.toString(counts));
jpayne@68 573 // }
jpayne@68 574 //
jpayne@68 575 // System.err.println(targetKeys+", "+counts.length+", "+valid+", "+len+", "+rounds+", "+Tools.sum(counts));
jpayne@68 576 //
jpayne@68 577 // return rounds;
jpayne@68 578 // }
jpayne@68 579
jpayne@68 580 //This can be done faster with bins.
jpayne@68 581 //Each bin contains all kmers with count x. When a bin is hit, one kmer moves to the next bin lower.
jpayne@68 582 //Alternately, expand the array into one physical kmer per count. Store the current counts in an IntMap. Remove key each time.
jpayne@68 583 public static long reduceRounds(final int[] counts0, final int[] counts, final int minCount, final int targetKeys, final Random randy){
jpayne@68 584 assert(minCount>=0) : minCount;
jpayne@68 585 long rounds=0;
jpayne@68 586 int valid=0;
jpayne@68 587 for(int x : counts){
jpayne@68 588 if(x>=minCount){valid++;}
jpayne@68 589 }
jpayne@68 590
jpayne@68 591 int len=counts.length;
jpayne@68 592 final long sum0=Tools.sum(counts);
jpayne@68 593 long sum=sum0;
jpayne@68 594 // System.err.println(targetKeys+", "+counts.length+", "+valid+", "+len+", "+rounds+", "+Tools.sum(counts)+", "+Arrays.toString(counts));
jpayne@68 595 for(; valid>targetKeys; rounds++){
jpayne@68 596 long posNum=(Long.MAX_VALUE&randy.nextLong())%sum;
jpayne@68 597 long sum2=0;
jpayne@68 598 int pos=0;
jpayne@68 599
jpayne@68 600 for(int i=0; i<counts.length; i++){
jpayne@68 601 int x=counts[i];
jpayne@68 602 if(x>0){
jpayne@68 603 sum2+=x;
jpayne@68 604 if(sum2>=posNum){
jpayne@68 605 pos=i;
jpayne@68 606 break;
jpayne@68 607 }
jpayne@68 608 }
jpayne@68 609 }
jpayne@68 610
jpayne@68 611 // for(int i=0; i<counts0.length; i++){
jpayne@68 612 // int x=counts0[i];
jpayne@68 613 // if(x>0){
jpayne@68 614 // sum2+=x;
jpayne@68 615 // if(sum2>=posNum){
jpayne@68 616 // pos=i;
jpayne@68 617 // break;
jpayne@68 618 // }
jpayne@68 619 // }
jpayne@68 620 // }
jpayne@68 621
jpayne@68 622 sum--;
jpayne@68 623
jpayne@68 624 assert(counts[pos]>0) : pos+"/"+len+": "+targetKeys+", "+counts.length+", "+valid+", "+len+", "+rounds+", "+Arrays.toString(counts);
jpayne@68 625 if(counts[pos]==minCount){valid--;}
jpayne@68 626 counts[pos]--;
jpayne@68 627 if(counts[pos]==0){
jpayne@68 628 len--;//shrink the array
jpayne@68 629 }
jpayne@68 630 // System.err.println(len+", "+pos+": "+Arrays.toString(counts));
jpayne@68 631 }
jpayne@68 632
jpayne@68 633 // System.err.println(targetKeys+", "+counts.length+", "+valid+", "+len+", "+rounds+", "+Tools.sum(counts));
jpayne@68 634
jpayne@68 635 return rounds;
jpayne@68 636 }
jpayne@68 637
jpayne@68 638 //This can be done faster with bins.
jpayne@68 639 //Each bin contains all kmers with count x. When a bin is hit, one kmer moves to the next bin lower.
jpayne@68 640 //Alternately, expand the array into one physical kmer per count. Store the current counts in an IntMap. Remove key each time.
jpayne@68 641 public static long reduceRoundsIM(final int[] counts0, final int[] expanded, final int minCount, final int targetKeys, final Random randy, final IntMap map){
jpayne@68 642 assert(minCount>=0) : minCount;
jpayne@68 643 long rounds=0;
jpayne@68 644 int valid=0;
jpayne@68 645 map.clear();
jpayne@68 646 for(int i=0, k=0; i<counts0.length; i++){
jpayne@68 647 int x=counts0[i];
jpayne@68 648 // counts[i]=counts0[i];
jpayne@68 649 if(x>=minCount){valid++;}
jpayne@68 650 map.put(i, x);
jpayne@68 651 for(int j=0; j<x; j++, k++){
jpayne@68 652 expanded[k]=i;
jpayne@68 653 }
jpayne@68 654 }
jpayne@68 655 assert(expanded.length==Tools.sum(counts0));
jpayne@68 656
jpayne@68 657 int len=expanded.length;
jpayne@68 658 // System.err.println(targetKeys+", "+counts.length+", "+valid+", "+len+", "+rounds+", "+Tools.sum(counts)+", "+Arrays.toString(counts));
jpayne@68 659 for(; valid>targetKeys; rounds++){
jpayne@68 660 final int pos=randy.nextInt(len);
jpayne@68 661 final int key=expanded[pos];
jpayne@68 662 final int x=map.get(key);
jpayne@68 663 assert(x>0);
jpayne@68 664
jpayne@68 665
jpayne@68 666 if(x==minCount){valid--;}
jpayne@68 667 map.put(key, x-1);
jpayne@68 668
jpayne@68 669 len--;//shrink the array
jpayne@68 670 // System.err.println("len="+len+", counts[len]="+counts[len]);
jpayne@68 671 // System.err.println("pos="+pos+", counts[pos]="+counts[pos]);
jpayne@68 672 expanded[pos]=expanded[len];//move the last element to the empty slot
jpayne@68 673 expanded[len]=0;
jpayne@68 674
jpayne@68 675 // System.err.println(len+", "+pos+": "+Arrays.toString(counts));
jpayne@68 676 }
jpayne@68 677
jpayne@68 678 // System.err.println(targetKeys+", "+counts.length+", "+valid+", "+len+", "+rounds+", "+Tools.sum(counts));
jpayne@68 679
jpayne@68 680 return rounds;
jpayne@68 681 }
jpayne@68 682
jpayne@68 683 /*--------------------------------------------------------------*/
jpayne@68 684 /*---------------- Inner Classes ----------------*/
jpayne@68 685 /*--------------------------------------------------------------*/
jpayne@68 686
jpayne@68 687 /** This class is static to prevent accidental writing to shared variables.
jpayne@68 688 * It is safe to remove the static modifier. */
jpayne@68 689 private class ProcessThread extends Thread {
jpayne@68 690
jpayne@68 691 //Constructor
jpayne@68 692 ProcessThread(final ConcurrentReadInputStream cris_, final ConcurrentReadOutputStream ros_, final int tid_, final int size){
jpayne@68 693 cris=cris_;
jpayne@68 694 ros=ros_;
jpayne@68 695 tid=tid_;
jpayne@68 696 localHeap=new SketchHeap(size, 0, true);
jpayne@68 697 }
jpayne@68 698
jpayne@68 699 //Called by start()
jpayne@68 700 @Override
jpayne@68 701 public void run(){
jpayne@68 702 //Do anything necessary prior to processing
jpayne@68 703
jpayne@68 704 //Process the reads
jpayne@68 705 processInner();
jpayne@68 706
jpayne@68 707 //Do anything necessary after processing
jpayne@68 708 dumpHeap();
jpayne@68 709
jpayne@68 710 //Indicate successful exit status
jpayne@68 711 success=true;
jpayne@68 712 }
jpayne@68 713
jpayne@68 714 /** Iterate through the reads */
jpayne@68 715 void processInner(){
jpayne@68 716
jpayne@68 717 //Grab the first ListNum of reads
jpayne@68 718 ListNum<Read> ln=cris.nextList();
jpayne@68 719 //Grab the actual read list from the ListNum
jpayne@68 720 ArrayList<Read> reads=(ln!=null ? ln.list : null);
jpayne@68 721
jpayne@68 722 //Check to ensure pairing is as expected
jpayne@68 723 if(reads!=null && !reads.isEmpty()){
jpayne@68 724 Read r=reads.get(0);
jpayne@68 725 // assert(ffin1.samOrBam() || (r.mate!=null)==cris.paired()); //Disabled due to non-static access
jpayne@68 726 }
jpayne@68 727
jpayne@68 728 //As long as there is a nonempty read list...
jpayne@68 729 while(ln!=null && reads!=null && reads.size()>0){//ln!=null prevents a compiler potential null access warning
jpayne@68 730 // if(verbose){outstream.println("Fetched "+reads.size()+" reads.");} //Disabled due to non-static access
jpayne@68 731
jpayne@68 732 //Loop through each read in the list
jpayne@68 733 for(int idx=0; idx<reads.size(); idx++){
jpayne@68 734 final Read r1=reads.get(idx);
jpayne@68 735 final Read r2=r1.mate;
jpayne@68 736
jpayne@68 737 //Validate reads in worker threads
jpayne@68 738 if(!r1.validated()){r1.validate(true);}
jpayne@68 739 if(r2!=null && !r2.validated()){r2.validate(true);}
jpayne@68 740
jpayne@68 741 //Track the initial length for statistics
jpayne@68 742 final int initialLength1=r1.length();
jpayne@68 743 final int initialLength2=r1.mateLength();
jpayne@68 744
jpayne@68 745 //Increment counters
jpayne@68 746 readsProcessedT+=r1.pairCount();
jpayne@68 747 basesProcessedT+=initialLength1+initialLength2;
jpayne@68 748
jpayne@68 749 //Reads are processed in this block.
jpayne@68 750 processReadPair(r1, r2);
jpayne@68 751 }
jpayne@68 752
jpayne@68 753 if(ros!=null){
jpayne@68 754 for(Read r1 : reads){
jpayne@68 755 readsOutT+=r1.pairCount();
jpayne@68 756 basesOutT+=r1.pairLength();
jpayne@68 757 }
jpayne@68 758
jpayne@68 759 //Output reads to the output stream
jpayne@68 760 if(ros!=null){ros.add(reads, ln.id);}
jpayne@68 761 }
jpayne@68 762
jpayne@68 763 //Notify the input stream that the list was used
jpayne@68 764 cris.returnList(ln);
jpayne@68 765 // if(verbose){outstream.println("Returned a list.");} //Disabled due to non-static access
jpayne@68 766
jpayne@68 767 //Fetch a new list
jpayne@68 768 ln=cris.nextList();
jpayne@68 769 reads=(ln!=null ? ln.list : null);
jpayne@68 770 }
jpayne@68 771
jpayne@68 772 //Notify the input stream that the final list was used
jpayne@68 773 if(ln!=null){
jpayne@68 774 if(ln.list!=null){ln.list.clear();}
jpayne@68 775 cris.returnList(ln.id, true);
jpayne@68 776 }
jpayne@68 777 }
jpayne@68 778
jpayne@68 779 /**
jpayne@68 780 * Process a read or a read pair.
jpayne@68 781 * @param r1 Read 1
jpayne@68 782 * @param r2 Read 2 (may be null)
jpayne@68 783 */
jpayne@68 784 void processReadPair(final Read r1, final Read r2){
jpayne@68 785 processReadNucleotide(r1);
jpayne@68 786 if(r2!=null){processReadNucleotide(r2);}
jpayne@68 787 }
jpayne@68 788
jpayne@68 789 void processReadNucleotide(final Read r){
jpayne@68 790 final byte[] bases=r.bases;
jpayne@68 791 final byte[] quals=r.quality;
jpayne@68 792 long kmer=0;
jpayne@68 793 long rkmer=0;
jpayne@68 794 int len=0;
jpayne@68 795 assert(!r.aminoacid());
jpayne@68 796
jpayne@68 797 final long min=minHashValue;
jpayne@68 798 localHeap.genomeSizeBases+=r.length();
jpayne@68 799 localHeap.genomeSequences++;
jpayne@68 800
jpayne@68 801 if(quals==null || (minProb<=0 && minQual<2)){
jpayne@68 802 for(int i=0; i<bases.length; i++){
jpayne@68 803 byte b=bases[i];
jpayne@68 804 long x=AminoAcid.baseToNumber[b];
jpayne@68 805 long x2=AminoAcid.baseToComplementNumber[b];
jpayne@68 806
jpayne@68 807 kmer=((kmer<<2)|x)&mask;
jpayne@68 808 rkmer=((rkmer>>>2)|(x2<<shift2))&mask;
jpayne@68 809
jpayne@68 810 if(x<0){len=0; rkmer=0;}else{len++;}
jpayne@68 811 if(len>=k){
jpayne@68 812 localHeap.genomeSizeKmers++;
jpayne@68 813 final long hashcode=hash(kmer, rkmer);
jpayne@68 814 if(hashcode>min){localHeap.add(hashcode);}
jpayne@68 815 }
jpayne@68 816 }
jpayne@68 817 }else{
jpayne@68 818 float prob=1;
jpayne@68 819 for(int i=0; i<bases.length; i++){
jpayne@68 820 final byte b=bases[i];
jpayne@68 821 final long x=AminoAcid.baseToNumber[b];
jpayne@68 822 final long x2=AminoAcid.baseToComplementNumber[b];
jpayne@68 823
jpayne@68 824 {//Quality-related stuff
jpayne@68 825 final byte q=quals[i];
jpayne@68 826 assert(q>=0) : Arrays.toString(quals)+"\n"+minProb+", "+minQual;
jpayne@68 827 prob=prob*align2.QualityTools.PROB_CORRECT[q];
jpayne@68 828 if(len>k){
jpayne@68 829 byte oldq=quals[i-k];
jpayne@68 830 prob=prob*align2.QualityTools.PROB_CORRECT_INVERSE[oldq];
jpayne@68 831 }
jpayne@68 832 if(x<0 || q<minQual){
jpayne@68 833 len=0;
jpayne@68 834 kmer=rkmer=0;
jpayne@68 835 prob=1;
jpayne@68 836 }else{
jpayne@68 837 len++;
jpayne@68 838 }
jpayne@68 839 }
jpayne@68 840
jpayne@68 841 kmer=((kmer<<2)|x)&mask;
jpayne@68 842 rkmer=((rkmer>>>2)|(x2<<shift2))&mask;
jpayne@68 843
jpayne@68 844 if(len>=k && prob>=minProb){
jpayne@68 845 localHeap.genomeSizeKmers++;
jpayne@68 846 localHeap.probSum+=prob;
jpayne@68 847 final long hashcode=hash(kmer, rkmer);
jpayne@68 848 if(hashcode>min){localHeap.checkAndAdd(hashcode);}
jpayne@68 849 }
jpayne@68 850 }
jpayne@68 851 }
jpayne@68 852 }
jpayne@68 853
jpayne@68 854 private void dumpHeap(){
jpayne@68 855 synchronized(sharedHeap){
jpayne@68 856 sharedHeap.add(localHeap);
jpayne@68 857 }
jpayne@68 858 }
jpayne@68 859
jpayne@68 860 /** Number of reads processed by this thread */
jpayne@68 861 protected long readsProcessedT=0;
jpayne@68 862 /** Number of bases processed by this thread */
jpayne@68 863 protected long basesProcessedT=0;
jpayne@68 864
jpayne@68 865 /** Number of reads retained by this thread */
jpayne@68 866 protected long readsOutT=0;
jpayne@68 867 /** Number of bases retained by this thread */
jpayne@68 868 protected long basesOutT=0;
jpayne@68 869
jpayne@68 870 /** True only if this thread has completed successfully */
jpayne@68 871 boolean success=false;
jpayne@68 872
jpayne@68 873 /** Shared input stream */
jpayne@68 874 private final ConcurrentReadInputStream cris;
jpayne@68 875 /** Shared output stream */
jpayne@68 876 private final ConcurrentReadOutputStream ros;
jpayne@68 877 /** Thread ID */
jpayne@68 878 final int tid;
jpayne@68 879
jpayne@68 880 final SketchHeap localHeap;
jpayne@68 881 }
jpayne@68 882
jpayne@68 883 /*--------------------------------------------------------------*/
jpayne@68 884 /*---------------- Fields ----------------*/
jpayne@68 885 /*--------------------------------------------------------------*/
jpayne@68 886
jpayne@68 887 /** Primary input file path */
jpayne@68 888 private String in1=null;
jpayne@68 889 /** Secondary input file path */
jpayne@68 890 private String in2=null;
jpayne@68 891
jpayne@68 892 private String qfin1=null;
jpayne@68 893 private String qfin2=null;
jpayne@68 894
jpayne@68 895 /** Primary output file path */
jpayne@68 896 private String out1=null;
jpayne@68 897 /** Secondary output file path */
jpayne@68 898 private String out2=null;
jpayne@68 899
jpayne@68 900 private String qfout1=null;
jpayne@68 901 private String qfout2=null;
jpayne@68 902
jpayne@68 903 /** Override input file extension */
jpayne@68 904 private String extin=null;
jpayne@68 905 /** Override output file extension */
jpayne@68 906 private String extout=null;
jpayne@68 907
jpayne@68 908 /*--------------------------------------------------------------*/
jpayne@68 909
jpayne@68 910 /** Number of reads processed */
jpayne@68 911 protected long readsProcessed=0;
jpayne@68 912 /** Number of bases processed */
jpayne@68 913 protected long basesProcessed=0;
jpayne@68 914
jpayne@68 915 /** Number of reads retained */
jpayne@68 916 protected long readsOut=0;
jpayne@68 917 /** Number of bases retained */
jpayne@68 918 protected long basesOut=0;
jpayne@68 919
jpayne@68 920 /** Quit after processing this many input reads; -1 means no limit */
jpayne@68 921 private long maxReads=-1;
jpayne@68 922
jpayne@68 923 private boolean paired=false;
jpayne@68 924 private int trials=25;
jpayne@68 925 private long seed=-1;
jpayne@68 926 private int maxExpandedLength=50000000;
jpayne@68 927
jpayne@68 928 /*--------------------------------------------------------------*/
jpayne@68 929 /*---------------- Final Fields ----------------*/
jpayne@68 930 /*--------------------------------------------------------------*/
jpayne@68 931
jpayne@68 932 /** Primary input file */
jpayne@68 933 private final FileFormat ffin1;
jpayne@68 934 /** Secondary input file */
jpayne@68 935 private final FileFormat ffin2;
jpayne@68 936
jpayne@68 937 /** Primary output file */
jpayne@68 938 private final FileFormat ffout1;
jpayne@68 939 /** Secondary output file */
jpayne@68 940 private final FileFormat ffout2;
jpayne@68 941
jpayne@68 942 private final SketchHeap sharedHeap;
jpayne@68 943 private final int heapSize;
jpayne@68 944 private final long targetKmers;
jpayne@68 945 private final int minCount;
jpayne@68 946
jpayne@68 947 final int shift;
jpayne@68 948 final int shift2;
jpayne@68 949 final long mask;
jpayne@68 950
jpayne@68 951 final float minProb;
jpayne@68 952 final byte minQual;
jpayne@68 953
jpayne@68 954 /*--------------------------------------------------------------*/
jpayne@68 955 /*---------------- Common Fields ----------------*/
jpayne@68 956 /*--------------------------------------------------------------*/
jpayne@68 957
jpayne@68 958 /** Print status messages to this output stream */
jpayne@68 959 private PrintStream outstream=System.err;
jpayne@68 960 /** Print verbose messages */
jpayne@68 961 public static boolean verbose=false;
jpayne@68 962 /** True if an error was encountered */
jpayne@68 963 public boolean errorState=false;
jpayne@68 964 /** Overwrite existing output files */
jpayne@68 965 private boolean overwrite=true;
jpayne@68 966 /** Append to existing output files */
jpayne@68 967 private boolean append=false;
jpayne@68 968 /** Reads are output in input order (not enabled) */
jpayne@68 969 private boolean ordered=true;
jpayne@68 970
jpayne@68 971 }