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Searched refs:initialLength2 (Results 1 – 25 of 45) sorted by relevance

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/dports/biology/bbmap/bbmap/current/hiseq/
H A DPlotFlowCell.java314 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()
H A DAnalyzeFlowCell.java490 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()
/dports/biology/bbmap/bbmap/current/jgi/
H A DFuseSequence.java104 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()
H A DFilterBySequence.java483 final int initialLength2=r1.mateLength();
487 basesProcessedT+=initialLength1+initialLength2;
495 basesOutT+=initialLength1+initialLength2;
606 final int initialLength2=r1.mateLength();
610 basesProcessedT+=initialLength1+initialLength2;
H A DMergeBarcodes.java232 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()
H A DReformatReads.java600 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()
H A DDemuxByName.java416 final int initialLength2=(r1.mateLength()); in process() local
444 basesOut+=initialLength2; in process()
455 basesOut+=initialLength2; in process()
493 basesProcessed+=initialLength2; in process()
H A DCorrelateBarcodes.java238 final int initialLength2=(r1.mateLength()); in process() local
258 basesTossed+=(initialLength1+initialLength2); in process()
272 basesProcessed+=initialLength2; in process()
H A DAdjustHomopolymers.java364 final int initialLength2=r1.mateLength(); in processList() local
368 basesProcessed+=initialLength1+initialLength2; in processList()
H A DKmerCountMulti.java405 final int initialLength2=r1.mateLength();
409 basesProcessedT+=initialLength1+initialLength2;
H A DPartitionReads.java319 final int initialLength2=(r1.mateLength()); in processInner() local
323 basesProcessed+=initialLength1+initialLength2; in processInner()
H A DReplaceHeaders.java321 final int initialLength2=(r1.mateLength()); in processInner() local
325 basesProcessed+=initialLength1+initialLength2; in processInner()
/dports/biology/bbmap/bbmap/current/tax/
H A DFilterByTaxa.java296 final int initialLength2=(r1.mateLength()); in processInner() local
300 basesProcessed+=initialLength1+initialLength2; in processInner()
306 basesOut+=initialLength1+initialLength2; in processInner()
H A DSplitByTaxa.java275 final int initialLength2=(r1.mateLength()); in processInner() local
279 basesProcessed+=initialLength1+initialLength2; in processInner()
/dports/biology/bbmap/bbmap/current/sort/
H A DShuffle2.java331 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()
H A DSortByName.java410 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()
/dports/biology/bbmap/bbmap/current/sketch/
H A DSketchMaker.java936 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()
H A DSketchMakerMini.java188 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()
/dports/biology/bbmap/bbmap/current/driver/
H A DFilterReadsByName.java306 final int initialLength2=(r1.mateLength()); in process() local
308 basesProcessed+=initialLength1+initialLength2; in process()
331 boolean keepThisRead=(initialLength1>=minLength || initialLength2>=minLength); in process()
H A DRenameAndMux.java415 final int initialLength2=(r1.mateLength()); in renameAndMergeOneFile() local
424 basesProcessed+=initialLength2; in renameAndMergeOneFile()
H A DLoadReads.java328 final int initialLength2=(r1.mateLength()); in processInner() local
332 basesProcessed+=initialLength1+initialLength2; in processInner()
/dports/biology/bbmap/bbmap/current/bloom/
H A DBloomFilterCorrectorWrapper.java673 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()
/dports/biology/bbmap/bbmap/current/template/
H A DA_Sample.java356 final int initialLength2=r1.mateLength(); in processList() local
360 basesProcessed+=initialLength1+initialLength2; in processList()
H A DBBTool_ST.java358 final int initialLength2=(r1.mateLength()); in processInner() local
366 basesProcessed+=initialLength2; in processInner()
H A DA_SampleMT.java431 final int initialLength2=r1.mateLength();
435 basesProcessedT+=initialLength1+initialLength2;

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