| /dports/biology/bbmap/bbmap/current/stream/ |
| H A D | SamReadStreamer.java | 158 readsProcessed+=pt.readsProcessedT; in processBytes()
206 readsProcessedT++; in makeReads()
223 protected long readsProcessedT=0; field in SamReadStreamer.ProcessThread
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| H A D | SamLineStreamer.java | 158 readsProcessed+=pt.readsProcessedT; in processBytes()
201 readsProcessedT++; in makeReads()
218 protected long readsProcessedT=0; field in SamLineStreamer.ProcessThread
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| /dports/biology/bbmap/bbmap/current/jgi/ |
| H A D | FilterBySequence.java | 362 readsLoaded+=pt.readsProcessedT;
409 readsProcessed+=pt.readsProcessedT;
486 readsProcessedT+=r1.pairCount();
533 protected long readsProcessedT=0;
609 readsProcessedT+=r1.pairCount();
650 protected long readsProcessedT=0;
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| H A D | KmerCountMulti.java | 283 readsProcessed+=pt.readsProcessedT;
408 readsProcessedT+=r1.pairCount();
444 protected long readsProcessedT=0;
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| H A D | FindPrimers.java | 278 readsProcessed+=pt.readsProcessedT; in accumulate()
368 readsProcessedT+=r.pairCount(); in processList()
565 protected long readsProcessedT=0; field in FindPrimers.ProcessThread
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| /dports/biology/bbmap/bbmap/current/cardinality/ |
| H A D | LogLogWrapper.java | 210 readsProcessed+=llt.readsProcessedT; in process()
310 readsProcessedT+=r.pairCount(); in runCris()
333 readsProcessedT+=r.pairCount(); in runSynth()
344 protected long readsProcessedT=0; field in LogLogWrapper.LogLogThread
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| /dports/biology/bbmap/bbmap/current/aligner/ |
| H A D | AllToAll.java | 286 readsProcessed+=pt.readsProcessedT;
341 readsProcessedT++;
366 protected long readsProcessedT=0;
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| /dports/biology/bbmap/bbmap/current/template/ |
| H A D | A_SampleSamStreamer.java | 355 readsProcessed+=pt.readsProcessedT;
427 readsProcessedT+=r.pairCount();
467 protected long readsProcessedT=0;
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| H A D | A_SampleMT.java | 340 readsProcessed+=pt.readsProcessedT;
434 readsProcessedT+=r1.pairCount();
465 protected long readsProcessedT=0;
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| /dports/biology/bbmap/bbmap/current/clump/ |
| H A D | PivotSet.java | 266 readsProcessed+=ht.readsProcessedT; in processInner()
294 readsProcessedT+=r1.pairCount(); in run()
326 protected long readsProcessedT=0; field in PivotSet.HashThread
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| H A D | KmerReduce.java | 293 readsProcessed+=ht.readsProcessedT; in processInner()
323 readsProcessedT++; in run()
344 protected long readsProcessedT=0; field in KmerReduce.HashThread
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| H A D | KmerSort3.java | 545 readsThisPass+=ft.readsProcessedT;
699 readsProcessedT+=readsThisGroup;
707 assert(readsProcessedT<=Integer.MAX_VALUE && readsProcessedT>=0);
728 protected long readsProcessedT=0;
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| H A D | KmerSort.java | 292 readsThisPass+=ht.readsProcessedT; in fetchReads1()
348 readsProcessedT+=1+r.mateCount(); in run()
420 protected long readsProcessedT=0; field in KmerSort.FetchThread1
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| H A D | KmerSplit.java | 362 readsProcessed+=ht.readsProcessedT; in splitReads()
409 readsProcessedT+=1+r.mateCount(); in run()
476 protected long readsProcessedT=0; field in KmerSplit.HashThread
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| /dports/biology/bbmap/bbmap/current/prok/ |
| H A D | MergeRibo_Fast.java | 313 readsProcessed+=pt.readsProcessedT;
401 readsProcessedT++;
451 protected long readsProcessedT=0;
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| H A D | SplitRibo.java | 358 readsProcessed+=pt.readsProcessedT;
458 readsProcessedT+=r1.pairCount();
535 protected long readsProcessedT=0;
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| H A D | RiboMaker.java | 419 readsProcessed+=pt.readsProcessedT;
543 readsProcessedT+=r1.pairCount();
596 protected long readsProcessedT=0;
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| H A D | MergeRibo.java | 386 readsProcessed+=pt.readsProcessedT; in accumulate()
482 readsProcessedT++; in processInput()
581 protected long readsProcessedT=0; field in MergeRibo.ProcessThread
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| /dports/biology/bbmap/bbmap/current/var2/ |
| H A D | Realign.java | 306 readsProcessed+=pt.readsProcessedT;
388 readsProcessedT+=r1.pairCount();
460 protected long readsProcessedT=0;
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| H A D | FilterSam.java | 401 readsProcessed+=pt.readsProcessedT;
500 readsProcessedT++;
568 readsProcessedT++;
672 protected long readsProcessedT=0; field in FilterSam
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| /dports/biology/bbmap/bbmap/current/sketch/ |
| H A D | KmerLimit.java | 346 readsProcessed+=pt.readsProcessedT;
426 readsProcessedT+=r1.pairCount();
548 protected long readsProcessedT=0;
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| H A D | BlacklistMaker.java | 378 readsProcessed+=pt.readsProcessedT;
655 readsProcessedT+=r1.pairCount();
828 protected long readsProcessedT=0;
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| /dports/biology/bbmap/bbmap/current/consensus/ |
| H A D | FixScaffoldGaps.java | 373 readsProcessed+=pt.readsProcessedT; in accumulate()
503 readsProcessedT+=r.pairCount(); in processList()
543 protected long readsProcessedT=0; field in FixScaffoldGaps.ProcessThread
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| H A D | ConsensusMaker.java | 580 readsProcessed+=pt.readsProcessedT;
674 readsProcessedT++;
759 protected long readsProcessedT=0;
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| /dports/biology/bbmap/bbmap/current/bloom/ |
| H A D | BloomFilterWrapper.java | 417 readsProcessed+=pt.readsProcessedT;
496 readsProcessedT+=r1.pairCount();
564 protected long readsProcessedT=0; local
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