Mercurial > repos > rliterman > csp2

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 16:23:26 -0400
parents
children
rev   line source
jpayne@68 1 package sketch;
jpayne@68 2
jpayne@68 3 import java.io.PrintStream;
jpayne@68 4 import java.util.ArrayList;
jpayne@68 5 import java.util.Collections;
jpayne@68 6 import java.util.HashMap;
jpayne@68 7 import java.util.Map.Entry;
jpayne@68 8 import java.util.concurrent.atomic.AtomicInteger;
jpayne@68 9
jpayne@68 10 import fileIO.ByteFile;
jpayne@68 11 import fileIO.ByteStreamWriter;
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.FASTQ;
jpayne@68 22 import stream.FastaReadInputStream;
jpayne@68 23 import stream.Read;
jpayne@68 24 import structures.ByteBuilder;
jpayne@68 25 import structures.FloatList;
jpayne@68 26 import tax.TaxNode;
jpayne@68 27 import tax.TaxTree;
jpayne@68 28 import template.Accumulator;
jpayne@68 29 import template.ThreadWaiter;
jpayne@68 30
jpayne@68 31 /**
jpayne@68 32 * Compares SSUs, all-to-all or fractional matrix.
jpayne@68 33 *
jpayne@68 34 * @author Brian Bushnell
jpayne@68 35 * @date December 2, 2019
jpayne@68 36 *
jpayne@68 37 */
jpayne@68 38 public class CompareSSU implements Accumulator<CompareSSU.ProcessThread> {
jpayne@68 39
jpayne@68 40 /*--------------------------------------------------------------*/
jpayne@68 41 /*---------------- Initialization ----------------*/
jpayne@68 42 /*--------------------------------------------------------------*/
jpayne@68 43
jpayne@68 44 /**
jpayne@68 45 * Code entrance from the command line.
jpayne@68 46 * @param args Command line arguments
jpayne@68 47 */
jpayne@68 48 public static void main(String[] args){
jpayne@68 49 //Start a timer immediately upon code entrance.
jpayne@68 50 Timer t=new Timer();
jpayne@68 51
jpayne@68 52 //Create an instance of this class
jpayne@68 53 CompareSSU x=new CompareSSU(args);
jpayne@68 54
jpayne@68 55 //Run the object
jpayne@68 56 x.process(t);
jpayne@68 57
jpayne@68 58 //Close the print stream if it was redirected
jpayne@68 59 Shared.closeStream(x.outstream);
jpayne@68 60 }
jpayne@68 61
jpayne@68 62 /**
jpayne@68 63 * Constructor.
jpayne@68 64 * @param args Command line arguments
jpayne@68 65 */
jpayne@68 66 public CompareSSU(String[] args){
jpayne@68 67
jpayne@68 68 {//Preparse block for help, config files, and outstream
jpayne@68 69 PreParser pp=new PreParser(args, getClass(), false);
jpayne@68 70 args=pp.args;
jpayne@68 71 outstream=pp.outstream;
jpayne@68 72 }
jpayne@68 73
jpayne@68 74 //Set shared static variables prior to parsing
jpayne@68 75 ReadWrite.USE_PIGZ=ReadWrite.USE_UNPIGZ=true;
jpayne@68 76 ReadWrite.MAX_ZIP_THREADS=Shared.threads();
jpayne@68 77
jpayne@68 78 {//Parse the arguments
jpayne@68 79 final Parser parser=parse(args);
jpayne@68 80 Parser.processQuality();
jpayne@68 81
jpayne@68 82 maxReads=parser.maxReads;
jpayne@68 83 overwrite=ReadStats.overwrite=parser.overwrite;
jpayne@68 84 append=ReadStats.append=parser.append;
jpayne@68 85
jpayne@68 86 in1=parser.in1;
jpayne@68 87
jpayne@68 88 out1=parser.out1;
jpayne@68 89 }
jpayne@68 90
jpayne@68 91 validateParams();
jpayne@68 92 if(in1==null){throw new RuntimeException("Error - at least one input file is required.");}
jpayne@68 93 FASTQ.FORCE_INTERLEAVED=FASTQ.TEST_INTERLEAVED=false;
jpayne@68 94 checkFileExistence(); //Ensure files can be read and written
jpayne@68 95 checkStatics(); //Adjust file-related static fields as needed for this program
jpayne@68 96
jpayne@68 97 //Create output FileFormat objects
jpayne@68 98 ffout1=FileFormat.testOutput(out1, FileFormat.TXT, null, true, overwrite, append, ordered);
jpayne@68 99
jpayne@68 100 tree=(treeFile==null) ? null : TaxTree.loadTaxTree(treeFile, outstream, true, false);
jpayne@68 101
jpayne@68 102 SSUMap.r16SFile=in1;
jpayne@68 103 if(SSUMap.r16SFile!=null){
jpayne@68 104 SSUMap.load(outstream);
jpayne@68 105 HashMap<Integer, byte[]> ssuMap=SSUMap.r16SMap;
jpayne@68 106 ssuList=new ArrayList<Read>(ssuMap.size());
jpayne@68 107 for(Entry<Integer, byte[]> e : ssuMap.entrySet()){
jpayne@68 108 int id=e.getKey();
jpayne@68 109 byte[] value=e.getValue();
jpayne@68 110 if(value.length>=minlen && value.length<=maxlen){
jpayne@68 111 Read r=new Read(value, null, id);//Sets numeric ID to TaxID.
jpayne@68 112 if(maxns<0 || r.countNocalls()<=maxns){
jpayne@68 113 ssuList.add(r);
jpayne@68 114 }
jpayne@68 115 }
jpayne@68 116 }
jpayne@68 117 Collections.shuffle(ssuList);
jpayne@68 118 }
jpayne@68 119 for(int i=0; i<idLists.length; i++){
jpayne@68 120 idLists[i]=new FloatList();
jpayne@68 121 }
jpayne@68 122 }
jpayne@68 123
jpayne@68 124 /*--------------------------------------------------------------*/
jpayne@68 125 /*---------------- Initialization Helpers ----------------*/
jpayne@68 126 /*--------------------------------------------------------------*/
jpayne@68 127
jpayne@68 128 /** Parse arguments from the command line */
jpayne@68 129 private Parser parse(String[] args){
jpayne@68 130
jpayne@68 131 //Create a parser object
jpayne@68 132 Parser parser=new Parser();
jpayne@68 133
jpayne@68 134 //Set any necessary Parser defaults here
jpayne@68 135 //parser.foo=bar;
jpayne@68 136
jpayne@68 137 //Parse each argument
jpayne@68 138 for(int i=0; i<args.length; i++){
jpayne@68 139 String arg=args[i];
jpayne@68 140
jpayne@68 141 //Break arguments into their constituent parts, in the form of "a=b"
jpayne@68 142 String[] split=arg.split("=");
jpayne@68 143 String a=split[0].toLowerCase();
jpayne@68 144 String b=split.length>1 ? split[1] : null;
jpayne@68 145 if(b!=null && b.equalsIgnoreCase("null")){b=null;}
jpayne@68 146
jpayne@68 147 if(a.equals("verbose")){
jpayne@68 148 verbose=Parse.parseBoolean(b);
jpayne@68 149 }else if(a.equals("tree")){
jpayne@68 150 treeFile=b;
jpayne@68 151 }else if(a.equals("ordered")){
jpayne@68 152 ordered=Parse.parseBoolean(b);
jpayne@68 153 }else if(a.equals("ata") || a.equals("alltoall")){
jpayne@68 154 allToAll=Parse.parseBoolean(b);
jpayne@68 155 }else if(a.equals("store") || a.equals("storeresults")){
jpayne@68 156 storeResults=Parse.parseBoolean(b);
jpayne@68 157 }else if(a.equals("minlen") || a.equals("maxlength")){
jpayne@68 158 minlen=Parse.parseIntKMG(b);
jpayne@68 159 }else if(a.equals("maxlen") || a.equals("maxlength")){
jpayne@68 160 maxlen=Parse.parseIntKMG(b);
jpayne@68 161 }else if(a.equalsIgnoreCase("maxns")){
jpayne@68 162 maxns=Parse.parseIntKMG(b);
jpayne@68 163 }else if(a.equals("parse_flag_goes_here")){
jpayne@68 164 long fake_variable=Parse.parseKMG(b);
jpayne@68 165 //Set a variable here
jpayne@68 166 }else if(parser.parse(arg, a, b)){//Parse standard flags in the parser
jpayne@68 167 //do nothing
jpayne@68 168 }else{
jpayne@68 169 outstream.println("Unknown parameter "+args[i]);
jpayne@68 170 assert(false) : "Unknown parameter "+args[i];
jpayne@68 171 }
jpayne@68 172 }
jpayne@68 173
jpayne@68 174 return parser;
jpayne@68 175 }
jpayne@68 176
jpayne@68 177 /** Ensure files can be read and written */
jpayne@68 178 private void checkFileExistence(){
jpayne@68 179 //Ensure output files can be written
jpayne@68 180 if(!Tools.testOutputFiles(overwrite, append, false, out1)){
jpayne@68 181 outstream.println((out1==null)+", "+out1);
jpayne@68 182 throw new RuntimeException("\n\noverwrite="+overwrite+"; Can't write to output file "+out1+"\n");
jpayne@68 183 }
jpayne@68 184
jpayne@68 185 //Ensure input files can be read
jpayne@68 186 if(!Tools.testInputFiles(false, true, in1)){
jpayne@68 187 throw new RuntimeException("\nCan't read some input files.\n");
jpayne@68 188 }
jpayne@68 189
jpayne@68 190 //Ensure that no file was specified multiple times
jpayne@68 191 if(!Tools.testForDuplicateFiles(true, in1, out1)){
jpayne@68 192 throw new RuntimeException("\nSome file names were specified multiple times.\n");
jpayne@68 193 }
jpayne@68 194 }
jpayne@68 195
jpayne@68 196 /** Adjust file-related static fields as needed for this program */
jpayne@68 197 private static void checkStatics(){
jpayne@68 198 //Adjust the number of threads for input file reading
jpayne@68 199 if(!ByteFile.FORCE_MODE_BF1 && !ByteFile.FORCE_MODE_BF2 && Shared.threads()>2){
jpayne@68 200 ByteFile.FORCE_MODE_BF2=true;
jpayne@68 201 }
jpayne@68 202
jpayne@68 203 assert(FastaReadInputStream.settingsOK());
jpayne@68 204 }
jpayne@68 205
jpayne@68 206 /** Ensure parameter ranges are within bounds and required parameters are set */
jpayne@68 207 private boolean validateParams(){
jpayne@68 208 return true;
jpayne@68 209 }
jpayne@68 210
jpayne@68 211 /*--------------------------------------------------------------*/
jpayne@68 212 /*---------------- Outer Methods ----------------*/
jpayne@68 213 /*--------------------------------------------------------------*/
jpayne@68 214
jpayne@68 215 /** Create read streams and process all data */
jpayne@68 216 void process(Timer t){
jpayne@68 217
jpayne@68 218 ByteStreamWriter bsw=makeBSW(ffout1);
jpayne@68 219 if(bsw!=null){
jpayne@68 220 bsw.forcePrint("#Level\tIdentity\tQueryID\tRefID\n");
jpayne@68 221 }
jpayne@68 222
jpayne@68 223 //Reset counters
jpayne@68 224 queriesProcessed=0;
jpayne@68 225 comparisons=0;
jpayne@68 226
jpayne@68 227 //Process the reads in separate threads
jpayne@68 228 spawnThreads(bsw);
jpayne@68 229
jpayne@68 230 if(verbose){outstream.println("Finished; closing streams.");}
jpayne@68 231
jpayne@68 232 //Close the read streams
jpayne@68 233 if(bsw!=null){errorState|=bsw.poisonAndWait();}
jpayne@68 234
jpayne@68 235 {
jpayne@68 236 ByteBuilder bb=new ByteBuilder();
jpayne@68 237 bb.append("\nLevel \tCount\tMean"+(storeResults ? "\tMedian\t90%ile\t10%ile\tSTDev" : "")+"\n");
jpayne@68 238 outstream.print(bb);
jpayne@68 239 final int minlen="superkingdom".length();
jpayne@68 240 for(int level=0; level<taxLevels; level++){
jpayne@68 241 if(counts[level]>0){
jpayne@68 242 bb.clear();
jpayne@68 243 bb.append(TaxTree.levelToStringExtended(level));
jpayne@68 244 while(bb.length()<minlen){bb.space();}
jpayne@68 245 bb.tab().append(counts[level]).tab();
jpayne@68 246 bb.append(sums[level]/counts[level]*100, 3);
jpayne@68 247 if(storeResults){
jpayne@68 248 FloatList list=idLists[level];
jpayne@68 249 list.sort();
jpayne@68 250 double stdev=list.stdev();
jpayne@68 251 double median=list.median();
jpayne@68 252 // double mode=list.mode();
jpayne@68 253 double percent90=list.percentile(0.9f);
jpayne@68 254 double percent10=list.percentile(0.1f);
jpayne@68 255 bb.tab().append(median*100, 3).tab().append(percent90*100, 3).tab().append(percent10*100, 3).tab().append(stdev*100, 3);
jpayne@68 256 }
jpayne@68 257 bb.nl();
jpayne@68 258 outstream.print(bb);
jpayne@68 259 }
jpayne@68 260 }
jpayne@68 261 }
jpayne@68 262
jpayne@68 263 //Report timing and results
jpayne@68 264 t.stop();
jpayne@68 265 outstream.println();
jpayne@68 266 outstream.println(Tools.timeQueriesComparisonsProcessed(t, queriesProcessed, comparisons, 8));
jpayne@68 267
jpayne@68 268 //Throw an exception of there was an error in a thread
jpayne@68 269 if(errorState){
jpayne@68 270 throw new RuntimeException(getClass().getName()+" terminated in an error state; the output may be corrupt.");
jpayne@68 271 }
jpayne@68 272 }
jpayne@68 273
jpayne@68 274 /*--------------------------------------------------------------*/
jpayne@68 275 /*---------------- Thread Management ----------------*/
jpayne@68 276 /*--------------------------------------------------------------*/
jpayne@68 277
jpayne@68 278 /** Spawn process threads */
jpayne@68 279 private void spawnThreads(ByteStreamWriter bsw){
jpayne@68 280
jpayne@68 281 //Do anything necessary prior to processing
jpayne@68 282
jpayne@68 283 //Determine how many threads may be used
jpayne@68 284 final int threads=Shared.threads();
jpayne@68 285
jpayne@68 286 //Fill a list with ProcessThreads
jpayne@68 287 ArrayList<ProcessThread> alpt=new ArrayList<ProcessThread>(threads);
jpayne@68 288 for(int i=0; i<threads; i++){
jpayne@68 289 alpt.add(new ProcessThread(bsw, i, threads));
jpayne@68 290 }
jpayne@68 291
jpayne@68 292 //Start the threads and wait for them to finish
jpayne@68 293 boolean success=ThreadWaiter.startAndWait(alpt, this);
jpayne@68 294 errorState&=!success;
jpayne@68 295
jpayne@68 296 //Do anything necessary after processing
jpayne@68 297
jpayne@68 298 }
jpayne@68 299
jpayne@68 300 @Override
jpayne@68 301 public final void accumulate(ProcessThread pt){
jpayne@68 302 queriesProcessed+=pt.querysProcessedT;
jpayne@68 303 comparisons+=pt.comparisonsT;
jpayne@68 304 errorState|=(!pt.success);
jpayne@68 305
jpayne@68 306 for(int i=0; i<taxLevels; i++){
jpayne@68 307 idLists[i].addAll(pt.idListsT[i]);
jpayne@68 308 counts[i]+=pt.countsT[i];
jpayne@68 309 sums[i]+=pt.sumsT[i];
jpayne@68 310 }
jpayne@68 311 }
jpayne@68 312
jpayne@68 313 @Override
jpayne@68 314 public final boolean success(){return !errorState;}
jpayne@68 315
jpayne@68 316 /*--------------------------------------------------------------*/
jpayne@68 317 /*---------------- Inner Methods ----------------*/
jpayne@68 318 /*--------------------------------------------------------------*/
jpayne@68 319
jpayne@68 320 private static ByteStreamWriter makeBSW(FileFormat ff){
jpayne@68 321 if(ff==null){return null;}
jpayne@68 322 ByteStreamWriter bsw=new ByteStreamWriter(ff);
jpayne@68 323 bsw.start();
jpayne@68 324 return bsw;
jpayne@68 325 }
jpayne@68 326
jpayne@68 327 /*--------------------------------------------------------------*/
jpayne@68 328 /*---------------- Inner Classes ----------------*/
jpayne@68 329 /*--------------------------------------------------------------*/
jpayne@68 330
jpayne@68 331 /** This class is static to prevent accidental writing to shared variables.
jpayne@68 332 * It is safe to remove the static modifier. */
jpayne@68 333 class ProcessThread extends Thread {
jpayne@68 334
jpayne@68 335 //Constructor
jpayne@68 336 ProcessThread(ByteStreamWriter bsw_, final int tid_, final int threads_){
jpayne@68 337 bsw=bsw_;
jpayne@68 338 threadID=tid_;
jpayne@68 339 threads=threads_;
jpayne@68 340 listCopy=new ArrayList<Read>(ssuList.size());
jpayne@68 341 listCopy.addAll(ssuList);
jpayne@68 342 for(int i=0; i<idListsT.length; i++){
jpayne@68 343 idListsT[i]=new FloatList();
jpayne@68 344 }
jpayne@68 345 }
jpayne@68 346
jpayne@68 347 //Called by start()
jpayne@68 348 @Override
jpayne@68 349 public void run(){
jpayne@68 350 //Do anything necessary prior to processing
jpayne@68 351
jpayne@68 352 //Process the reads
jpayne@68 353 processInner();
jpayne@68 354
jpayne@68 355 //Do anything necessary after processing
jpayne@68 356
jpayne@68 357 //Indicate successful exit status
jpayne@68 358 success=true;
jpayne@68 359 }
jpayne@68 360
jpayne@68 361 /** Iterate through the reads */
jpayne@68 362 void processInner(){
jpayne@68 363 final long limit=Tools.min(ssuList.size(), (maxReads>0 ? maxReads : Integer.MAX_VALUE));
jpayne@68 364
jpayne@68 365 for(int num=next.getAndIncrement(); num<limit; num=next.getAndIncrement()){
jpayne@68 366 Read r=ssuList.get(num);
jpayne@68 367 processRead(r);
jpayne@68 368 }
jpayne@68 369 }
jpayne@68 370
jpayne@68 371 void processRead(Read query){
jpayne@68 372 if(query.numericID<1){return;}//invalid TID
jpayne@68 373 final int qid=(int)query.numericID;
jpayne@68 374 if(tree.getNode(qid)==null) {return;}
jpayne@68 375 if(querysProcessedT%5==0) {
jpayne@68 376 Collections.shuffle(listCopy);
jpayne@68 377 }
jpayne@68 378 querysProcessedT++;
jpayne@68 379
jpayne@68 380 ByteBuilder bb=new ByteBuilder();
jpayne@68 381
jpayne@68 382 long seen=0;
jpayne@68 383 for(Read ref :listCopy){
jpayne@68 384 int rid=(int)ref.numericID;
jpayne@68 385 if(rid!=qid && rid>0 && tree.getNode(rid)!=null){
jpayne@68 386 int aid=tree.commonAncestor(qid, rid);
jpayne@68 387 if(aid>0){
jpayne@68 388 TaxNode tn=tree.getNode(aid);
jpayne@68 389 if(tn.isRanked()){
jpayne@68 390 int level=tn.levelExtended;
jpayne@68 391 long mask=1L<<level;
jpayne@68 392 if(allToAll || ((mask&printLevels)!=0 && (mask&seen)==0)){
jpayne@68 393 seen|=mask;
jpayne@68 394 float identity=compare(query, ref, level);
jpayne@68 395 bb.append(TaxTree.levelToStringExtended(level)).tab().append(identity, 6);
jpayne@68 396 bb.tab().append(qid).tab().append(rid).nl();
jpayne@68 397 }
jpayne@68 398 }
jpayne@68 399 }
jpayne@68 400 }
jpayne@68 401 }
jpayne@68 402 if(bsw!=null){
jpayne@68 403 bsw.addJob(bb);
jpayne@68 404 }
jpayne@68 405 }
jpayne@68 406
jpayne@68 407 float compare(Read query, Read ref, int level){
jpayne@68 408 comparisonsT++;
jpayne@68 409 float identity=SketchObject.align(query.bases, ref.bases);
jpayne@68 410 if(storeResults){idListsT[level].add(identity);}
jpayne@68 411 countsT[level]++;
jpayne@68 412 sumsT[level]+=identity;
jpayne@68 413 return identity;
jpayne@68 414 }
jpayne@68 415
jpayne@68 416 /** Number of reads processed by this thread */
jpayne@68 417 protected long querysProcessedT=0;
jpayne@68 418 /** Number of bases processed by this thread */
jpayne@68 419 protected long comparisonsT=0;
jpayne@68 420
jpayne@68 421 /** True only if this thread has completed successfully */
jpayne@68 422 boolean success=false;
jpayne@68 423
jpayne@68 424 /** Shared output stream */
jpayne@68 425 private final ByteStreamWriter bsw;
jpayne@68 426 /** Thread ID */
jpayne@68 427 final int threadID;
jpayne@68 428
jpayne@68 429 final int threads;
jpayne@68 430
jpayne@68 431 ArrayList<Read> listCopy;
jpayne@68 432
jpayne@68 433 final FloatList[] idListsT=new FloatList[taxLevels];
jpayne@68 434 long[] countsT=new long[taxLevels];
jpayne@68 435 double[] sumsT=new double[taxLevels];
jpayne@68 436 }
jpayne@68 437
jpayne@68 438 /*--------------------------------------------------------------*/
jpayne@68 439 /*---------------- Fields ----------------*/
jpayne@68 440 /*--------------------------------------------------------------*/
jpayne@68 441
jpayne@68 442 /** Primary input file path */
jpayne@68 443 private String in1=null;
jpayne@68 444
jpayne@68 445 private String treeFile="auto";
jpayne@68 446
jpayne@68 447 /** Primary output file path */
jpayne@68 448 private String out1=null;
jpayne@68 449
jpayne@68 450 public static ArrayList<Read> ssuList=null;
jpayne@68 451
jpayne@68 452 final static int taxLevels=TaxTree.numTaxLevelNamesExtended;
jpayne@68 453 static final String[] printLevelsArray=new String[] {"strain", "species", "genus", "family", "order", "class", "phylum", "superkingdom", "life"};
jpayne@68 454 static final long printLevels=makePrintLevels(printLevelsArray);
jpayne@68 455
jpayne@68 456 private final TaxTree tree;
jpayne@68 457
jpayne@68 458 private static final long makePrintLevels(String[] names){
jpayne@68 459 long mask=0;
jpayne@68 460 for(String s : names){
jpayne@68 461 int level=TaxTree.stringToLevelExtended(s);
jpayne@68 462 mask|=(1L<<level);
jpayne@68 463 }
jpayne@68 464 return mask;
jpayne@68 465 }
jpayne@68 466
jpayne@68 467 private FloatList[] idLists=new FloatList[taxLevels];
jpayne@68 468 private long[] counts=new long[taxLevels];
jpayne@68 469 private double[] sums=new double[taxLevels];
jpayne@68 470
jpayne@68 471 private int minlen=0;
jpayne@68 472 private int maxlen=Integer.MAX_VALUE;
jpayne@68 473 private int maxns=-1;
jpayne@68 474
jpayne@68 475 /*--------------------------------------------------------------*/
jpayne@68 476
jpayne@68 477 /** Number of reads processed */
jpayne@68 478 protected long queriesProcessed=0;
jpayne@68 479 /** Number of bases processed */
jpayne@68 480 protected long comparisons=0;
jpayne@68 481
jpayne@68 482 /** Quit after processing this many input reads; -1 means no limit */
jpayne@68 483 private long maxReads=-1;
jpayne@68 484
jpayne@68 485 private AtomicInteger next=new AtomicInteger(0);
jpayne@68 486
jpayne@68 487 private boolean allToAll=false;
jpayne@68 488 private boolean storeResults=false;
jpayne@68 489
jpayne@68 490 /*--------------------------------------------------------------*/
jpayne@68 491 /*---------------- Final Fields ----------------*/
jpayne@68 492 /*--------------------------------------------------------------*/
jpayne@68 493
jpayne@68 494 /** Primary output file */
jpayne@68 495 private final FileFormat ffout1;
jpayne@68 496
jpayne@68 497 /*--------------------------------------------------------------*/
jpayne@68 498 /*---------------- Common Fields ----------------*/
jpayne@68 499 /*--------------------------------------------------------------*/
jpayne@68 500
jpayne@68 501 /** Print status messages to this output stream */
jpayne@68 502 private PrintStream outstream=System.err;
jpayne@68 503 /** Print verbose messages */
jpayne@68 504 public static boolean verbose=false;
jpayne@68 505 /** True if an error was encountered */
jpayne@68 506 public boolean errorState=false;
jpayne@68 507 /** Overwrite existing output files */
jpayne@68 508 private boolean overwrite=false;
jpayne@68 509 /** Append to existing output files */
jpayne@68 510 private boolean append=false;
jpayne@68 511 /** Reads are output in input order */
jpayne@68 512 private boolean ordered=false;
jpayne@68 513
jpayne@68 514 }