| /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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