/dports/biology/bbmap/bbmap/current/hiseq/ |
H A D | PlotFlowCell.java | 314 final int initialLength2=(r1.mateLength()); in loadKmersInner() local 324 if(initialLength2>=k && randy.nextBoolean()){ in loadKmersInner() 325 final long kmer=toKmer(r2.bases, randy.nextInt(initialLength2-k2), k); in loadKmersInner() 382 final int initialLength2=(r1.mateLength()); in fillTilesInner() local 386 basesProcessed+=initialLength1+initialLength2; in fillTilesInner()
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H A D | AnalyzeFlowCell.java | 490 final int initialLength2=(r1.mateLength()); in processInner() local 494 basesProcessed+=initialLength1+initialLength2; in processInner() 502 basesDiscarded+=initialLength1+initialLength2; in processInner() 568 final int initialLength2=(r1.mateLength()); in loadKmersInner() local 578 if(initialLength2>=k && randy.nextBoolean()){ in loadKmersInner() 579 final long kmer=toKmer(r2.bases, r2.quality, randy.nextInt(initialLength2-k2), k); in loadKmersInner() 636 final int initialLength2=(r1.mateLength()); in fillTilesInner() local 640 basesProcessed+=initialLength1+initialLength2; in fillTilesInner()
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/dports/biology/bbmap/bbmap/current/jgi/ |
H A D | FuseSequence.java | 104 final int initialLength2=(r1.mateLength()); in processInner() local 112 basesProcessed+=initialLength2; in processInner() 115 …if(!fusePairs && maxlen>0 && bases.length>0 && bases.length+initialLength1+initialLength2+npad>max… in processInner()
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H A D | FilterBySequence.java | 483 final int initialLength2=r1.mateLength(); 487 basesProcessedT+=initialLength1+initialLength2; 495 basesOutT+=initialLength1+initialLength2; 606 final int initialLength2=r1.mateLength(); 610 basesProcessedT+=initialLength1+initialLength2;
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H A D | MergeBarcodes.java | 232 final int initialLength2=(r1.mateLength()); in loadBarcodes() local 240 basesProcessed+=initialLength2; in loadBarcodes() 333 final int initialLength2=(r1.mateLength()); in mergeWithMap() local 342 basesProcessed+=initialLength2; in mergeWithMap()
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H A D | ReformatReads.java | 600 final int initialLength2=(r1.mateLength()); in process() local 603 final int minlen2=(int)Tools.max(initialLength2*minLenFraction, minReadLength); in process() 675 basesProcessed+=initialLength2; in process() 800 idfilteredBasesT+=initialLength2; in process() 853 unmappedBasesT+=initialLength2; in process() 866 unmappedBasesT+=initialLength2; in process() 871 if(filterGC && (initialLength1>0 || initialLength2>0)){ in process() 873 float gc2=(initialLength2>0 ? r2.gc() : gc1); in process() 880 gc=(gc1*initialLength1+gc2*initialLength2)/(initialLength1+initialLength2); in process() 891 badGcBasesT+=initialLength2; in process()
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H A D | DemuxByName.java | 416 final int initialLength2=(r1.mateLength()); in process() local 444 basesOut+=initialLength2; in process() 455 basesOut+=initialLength2; in process() 493 basesProcessed+=initialLength2; in process()
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H A D | CorrelateBarcodes.java | 238 final int initialLength2=(r1.mateLength()); in process() local 258 basesTossed+=(initialLength1+initialLength2); in process() 272 basesProcessed+=initialLength2; in process()
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H A D | AdjustHomopolymers.java | 364 final int initialLength2=r1.mateLength(); in processList() local 368 basesProcessed+=initialLength1+initialLength2; in processList()
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H A D | KmerCountMulti.java | 405 final int initialLength2=r1.mateLength(); 409 basesProcessedT+=initialLength1+initialLength2;
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H A D | PartitionReads.java | 319 final int initialLength2=(r1.mateLength()); in processInner() local 323 basesProcessed+=initialLength1+initialLength2; in processInner()
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H A D | ReplaceHeaders.java | 321 final int initialLength2=(r1.mateLength()); in processInner() local 325 basesProcessed+=initialLength1+initialLength2; in processInner()
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/dports/biology/bbmap/bbmap/current/tax/ |
H A D | FilterByTaxa.java | 296 final int initialLength2=(r1.mateLength()); in processInner() local 300 basesProcessed+=initialLength1+initialLength2; in processInner() 306 basesOut+=initialLength1+initialLength2; in processInner()
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H A D | SplitByTaxa.java | 275 final int initialLength2=(r1.mateLength()); in processInner() local 279 basesProcessed+=initialLength1+initialLength2; in processInner()
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/dports/biology/bbmap/bbmap/current/sort/ |
H A D | Shuffle2.java | 331 final int initialLength2=(r1.mateLength()); in processInner() local 335 basesProcessed+=initialLength1+initialLength2; in processInner() 336 maxLengthObserved=Tools.max(maxLengthObserved, initialLength1, initialLength2); in processInner() 338 if(minlen<1 || initialLength1>=minlen || initialLength2>=minlen){ in processInner()
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H A D | SortByName.java | 410 final int initialLength2=(r1.mateLength()); in processInner() local 414 basesProcessed+=initialLength1+initialLength2; in processInner() 415 maxLengthObserved=Tools.max(maxLengthObserved, initialLength1, initialLength2); in processInner() 417 if(minlen<1 || initialLength1>=minlen || initialLength2>=minlen){ in processInner()
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/dports/biology/bbmap/bbmap/current/sketch/ |
H A D | SketchMaker.java | 936 final int initialLength2=r1.mateLength(); in processReadPair() local 941 basesProcessedT+=initialLength1+initialLength2; in processReadPair() 943 if(initialLength1<k && initialLength2<k){return;} in processReadPair() 1001 expectedBases=initialLength1+initialLength2; in processReadPair() 1015 expectedBases=unitSizeBases>-1 ? unitSizeBases : initialLength1+initialLength2; in processReadPair() 1029 expectedBases=unitSizeBases>-1 ? unitSizeBases : initialLength1+initialLength2; in processReadPair() 1076 if(initialLength2>=k){smm.processRead(r2);} in processReadPair()
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H A D | SketchMakerMini.java | 188 final int initialLength2=r1.mateLength(); in processReadPair() local 192 basesProcessed+=initialLength1+initialLength2; in processReadPair() 195 int expectedSize=toSketchSize(initialLength1+initialLength2, -1, -1, targetSketchSize); in processReadPair()
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/dports/biology/bbmap/bbmap/current/driver/ |
H A D | FilterReadsByName.java | 306 final int initialLength2=(r1.mateLength()); in process() local 308 basesProcessed+=initialLength1+initialLength2; in process() 331 boolean keepThisRead=(initialLength1>=minLength || initialLength2>=minLength); in process()
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H A D | RenameAndMux.java | 415 final int initialLength2=(r1.mateLength()); in renameAndMergeOneFile() local 424 basesProcessed+=initialLength2; in renameAndMergeOneFile()
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H A D | LoadReads.java | 328 final int initialLength2=(r1.mateLength()); in processInner() local 332 basesProcessed+=initialLength1+initialLength2; in processInner()
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/dports/biology/bbmap/bbmap/current/bloom/ |
H A D | BloomFilterCorrectorWrapper.java | 673 final int initialLength2=r1.mateLength(); in processInner() local 677 basesProcessedT+=initialLength1+initialLength2; in processInner() 689 …if(testMerge && !corrector.mergeOK(r1, initialLength1, initialLength2, kmers, testMergeWidth, test… in processInner() 706 …if(!testMerge || corrector.mergeOK(merged, initialLength1, initialLength2, kmers, testMergeWidth, … in processInner() 723 final int len=Tools.min(r1.length(), initialLength2); in processInner()
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/dports/biology/bbmap/bbmap/current/template/ |
H A D | A_Sample.java | 356 final int initialLength2=r1.mateLength(); in processList() local 360 basesProcessed+=initialLength1+initialLength2; in processList()
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H A D | BBTool_ST.java | 358 final int initialLength2=(r1.mateLength()); in processInner() local 366 basesProcessed+=initialLength2; in processInner()
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H A D | A_SampleMT.java | 431 final int initialLength2=r1.mateLength(); 435 basesProcessedT+=initialLength1+initialLength2;
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