/dports/biology/bbmap/bbmap/current/template/ |
H A D | A_Sample_Generator.java | 322 readsOut+=pt.readsOutT; in waitForThreads() 431 readsOutT+=r.pairCount(); in generateList() 448 protected long readsOutT=0; field in A_Sample_Generator.ProcessThread
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H A D | A_SampleSamStreamer.java | 357 readsOut+=pt.readsOutT; 436 readsOutT++; 472 protected long readsOutT=0;
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H A D | A_SampleMT.java | 342 readsOut+=pt.readsOutT; 443 readsOutT+=r1.pairCount(); 470 protected long readsOutT=0;
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/dports/biology/bbmap/bbmap/current/prok/ |
H A D | SplitRibo.java | 360 Tools.add(readsOut, pt.readsOutT); 464 readsOutT[type]+=r1.pairCount(); 540 protected long[] readsOutT=new long[numTypes];
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H A D | RiboMaker.java | 421 readsOut+=pt.readsOutT; 601 protected long readsOutT=0;
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/dports/biology/bbmap/bbmap/current/sketch/ |
H A D | KmerLimit.java | 348 readsOut+=pt.readsOutT; 437 readsOutT+=r1.pairCount(); 553 protected long readsOutT=0; local
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H A D | KmerLimit2.java | 391 readsOut+=pt.readsOutT; 473 readsOut+=pt.readsOutT; 755 readsOutT+=r1.pairCount(); in processInner() 866 protected long readsOutT=0; field in KmerLimit2.ProcessThread
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/dports/biology/bbmap/bbmap/current/var2/ |
H A D | FilterSam.java | 407 readsOut+=pt.readsOutT; 508 readsOutT++; 576 readsOutT++; 684 protected long readsOutT=0; field in FilterSam
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/dports/biology/bbmap/bbmap/current/jgi/ |
H A D | FilterBySequence.java | 411 readsOut+=pt.readsOutT; 494 readsOutT+=r1.pairCount(); 538 protected long readsOutT=0;
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H A D | FindPrimers.java | 280 readsOut+=pt.readsOutT; in accumulate() 377 readsOutT+=r.pairCount(); in processList() 570 protected long readsOutT=0; field in FindPrimers.ProcessThread
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H A D | BBDuk2.java | 1622 readsOut+=pt.readsOutT; in spawnProcessThreads() 2386 readsOutT++; in run() 2390 readsOutT++; in run() 3262 private long readsOutT=0; field in BBDuk2.ProcessThread
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/dports/biology/bbmap/bbmap/current/consensus/ |
H A D | FixScaffoldGaps.java | 375 readsOut+=pt.readsOutT; in accumulate() 533 readsOutT++; in processRead() 548 protected long readsOutT=0; field in FixScaffoldGaps.ProcessThread
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H A D | Lilypad.java | 381 readsOut+=pt.readsOutT; in accumulate() 552 readsOutT++; in processRead() 565 readsOutT++; in processRead() 580 protected long readsOutT=0; field in Lilypad.ProcessThread
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/dports/biology/bbmap/bbmap/current/gff/ |
H A D | CutGff.java | 633 readsOut+=pt.readsOutT; in accumulate() 700 readsOutT++; in processFileT() 707 readsOutT++; in processFileT() 721 protected long readsOutT=0; field in CutGff.ProcessThread
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/dports/biology/bbmap/bbmap/current/bloom/ |
H A D | BloomFilterWrapper.java | 419 readsOut+=pt.readsOutT; 520 readsOutT+=r1.pairCount(); 569 protected long readsOutT=0; local
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H A D | BloomFilterCorrectorWrapper.java | 564 readsOut+=pt.readsOutT; in spawnThreads() 761 readsOutT+=r1.pairCount(); in processInner() 831 protected long readsOutT=0; field in BloomFilterCorrectorWrapper.ProcessThread
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/dports/biology/bbmap/bbmap/current/icecream/ |
H A D | IceCreamMaker.java | 428 readsOut+=pt.readsOutT; in waitForThreads() 741 readsOutT+=r.pairCount(); in generateZMW() 844 protected long readsOutT=0;
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H A D | ReformatPacBio.java | 542 readsOut+=pt.readsOutT; in waitForThreads() 1210 readsOutT++; in outputReads() 1235 protected long readsOutT=0; field in ReformatPacBio.ProcessThread
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H A D | IceCreamFinder.java | 638 readsOut+=pt.readsOutT; 1136 readsOutT++; 1147 readsOutT++; 1560 protected long readsOutT=0; field in IceCreamFinder
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