| /dports/biology/bbmap/bbmap/current/stream/ |
| H A D | SamReadStreamer.java | 159 basesProcessed+=pt.basesProcessedT; in processBytes()
207 basesProcessedT+=r.length(); in makeReads()
225 protected long basesProcessedT=0; field in SamReadStreamer.ProcessThread
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| H A D | SamLineStreamer.java | 159 basesProcessed+=pt.basesProcessedT; in processBytes()
202 basesProcessedT+=(sl.seq==null ? 0 : sl.length()); in makeReads()
220 protected long basesProcessedT=0; field in SamLineStreamer.ProcessThread
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| /dports/biology/bbmap/bbmap/current/jgi/ |
| H A D | FilterBySequence.java | 363 basesLoaded+=pt.basesProcessedT;
410 basesProcessed+=pt.basesProcessedT;
487 basesProcessedT+=initialLength1+initialLength2;
535 protected long basesProcessedT=0;
610 basesProcessedT+=initialLength1+initialLength2;
652 protected long basesProcessedT=0;
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| H A D | KmerCountMulti.java | 284 basesProcessed+=pt.basesProcessedT;
409 basesProcessedT+=initialLength1+initialLength2;
446 protected long basesProcessedT=0;
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| H A D | FindPrimers.java | 279 basesProcessed+=pt.basesProcessedT; in accumulate()
369 basesProcessedT+=initialLength1; in processList()
567 protected long basesProcessedT=0; field in FindPrimers.ProcessThread
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| /dports/biology/bbmap/bbmap/current/cardinality/ |
| H A D | LogLogWrapper.java | 211 basesProcessed+=llt.basesProcessedT; in process()
311 basesProcessedT+=r.pairLength(); in runCris()
334 basesProcessedT+=r.pairLength(); in runSynth()
345 protected long basesProcessedT=0; field in LogLogWrapper.LogLogThread
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| /dports/biology/bbmap/bbmap/current/aligner/ |
| H A D | AllToAll.java | 287 basesProcessed+=pt.basesProcessedT;
342 basesProcessedT+=query.length();
368 protected long basesProcessedT=0;
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| /dports/biology/bbmap/bbmap/current/template/ |
| H A D | A_SampleSamStreamer.java | 356 basesProcessed+=pt.basesProcessedT;
428 basesProcessedT+=initialLength;
469 protected long basesProcessedT=0;
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| H A D | A_SampleMT.java | 341 basesProcessed+=pt.basesProcessedT;
435 basesProcessedT+=initialLength1+initialLength2;
467 protected long basesProcessedT=0;
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| /dports/biology/bbmap/bbmap/current/clump/ |
| H A D | PivotSet.java | 267 basesProcessed+=ht.basesProcessedT; in processInner()
295 basesProcessedT+=r1.pairLength(); in run()
327 protected long basesProcessedT=0; field in PivotSet.HashThread
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| H A D | KmerReduce.java | 294 basesProcessed+=ht.basesProcessedT; in processInner()
324 basesProcessedT+=r.length(); in run()
345 protected long basesProcessedT=0; field in KmerReduce.HashThread
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| H A D | KmerSort.java | 293 basesProcessed+=ht.basesProcessedT; in fetchReads1()
349 basesProcessedT+=r.length()+r.mateLength(); in run()
421 protected long basesProcessedT=0; field in KmerSort.FetchThread1
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| H A D | KmerSplit.java | 363 basesProcessed+=ht.basesProcessedT; in splitReads()
410 basesProcessedT+=r.length()+r.mateLength(); in run()
477 protected long basesProcessedT=0; field in KmerSplit.HashThread
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| /dports/biology/bbmap/bbmap/current/prok/ |
| H A D | MergeRibo_Fast.java | 314 basesProcessed+=pt.basesProcessedT;
402 basesProcessedT+=initialLength1;
453 protected long basesProcessedT=0;
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| H A D | SplitRibo.java | 359 basesProcessed+=pt.basesProcessedT;
459 basesProcessedT+=initialLength1+initialLength2;
537 protected long basesProcessedT=0;
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| H A D | RiboMaker.java | 420 basesProcessed+=pt.basesProcessedT;
544 basesProcessedT+=initialLength1+initialLength2;
598 protected long basesProcessedT=0;
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| H A D | MergeRibo.java | 387 basesProcessed+=pt.basesProcessedT; in accumulate()
483 basesProcessedT+=initialLength1; in processInput()
583 protected long basesProcessedT=0; field in MergeRibo.ProcessThread
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| /dports/biology/bbmap/bbmap/current/var2/ |
| H A D | Realign.java | 307 basesProcessed+=pt.basesProcessedT;
389 basesProcessedT+=initialLength1+initialLength2;
462 protected long basesProcessedT=0;
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| H A D | FilterSam.java | 402 basesProcessed+=pt.basesProcessedT;
501 basesProcessedT+=initialLength1;
569 basesProcessedT+=initialLength1;
674 protected long basesProcessedT=0; field in FilterSam
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| /dports/biology/bbmap/bbmap/current/sketch/ |
| H A D | KmerLimit.java | 347 basesProcessed+=pt.basesProcessedT;
427 basesProcessedT+=initialLength1+initialLength2;
550 protected long basesProcessedT=0; local
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| H A D | BlacklistMaker.java | 379 basesProcessed+=pt.basesProcessedT;
656 basesProcessedT+=initialLength1+initialLength2;
830 protected long basesProcessedT=0;
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| H A D | KmerLimit2.java | 390 basesProcessed+=pt.basesProcessedT;
747 basesProcessedT+=initialLength1+initialLength2; in processInner()
863 protected long basesProcessedT=0; field in KmerLimit2.ProcessThread
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| /dports/biology/bbmap/bbmap/current/consensus/ |
| H A D | FixScaffoldGaps.java | 374 basesProcessed+=pt.basesProcessedT; in accumulate()
504 basesProcessedT+=initialLength; in processList()
545 protected long basesProcessedT=0; field in FixScaffoldGaps.ProcessThread
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| H A D | ConsensusMaker.java | 581 basesProcessed+=pt.basesProcessedT;
675 basesProcessedT+=initialLength;
761 protected long basesProcessedT=0;
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| /dports/biology/bbmap/bbmap/current/bloom/ |
| H A D | BloomFilterWrapper.java | 418 basesProcessed+=pt.basesProcessedT;
497 basesProcessedT+=initialLength1+initialLength2;
566 protected long basesProcessedT=0; local
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