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Searched refs:fillAndScoreLimited (Results 1 – 22 of 22) sorted by relevance

/dports/biology/bbmap/bbmap/current/pacbio/
H A DRemoveAdapters2.java438 int[] rvec=msa.fillAndScoreLimited(query2, array, i, j, minSwScoreSuspect);
450 rvec=msa.fillAndScoreLimited(query2, array, stop, stop+window, minSwScoreSuspect);
458 …rvec=msa2.fillAndScoreLimited(query2, array, Tools.max(0, start-4), Tools.min(stop+4, array.length…
475 int[] rvec=msa.fillAndScoreLimited(query1, array, i, j, minSwScoreSuspect);
486 rvec=msa.fillAndScoreLimited(query1, array, stop, stop+window, minSwScoreSuspect);
494 …rvec=msa2.fillAndScoreLimited(query1, array, Tools.max(0, start-4), Tools.min(stop+4, array.length…
H A DRemoveAdapters3.java394 int[] rvec=msa.fillAndScoreLimited(query2, array, i, j, minSwScoreSuspect);
404 rvec=msa.fillAndScoreLimited(query2, array, stop, stop+window, minSwScoreSuspect);
425 int[] rvec=msa.fillAndScoreLimited(query1, array, i, j, minSwScoreSuspect);
434 rvec=msa.fillAndScoreLimited(query1, array, stop, stop+window, minSwScoreSuspect);
511 int[] rvec=msaR.fillAndScoreLimited(rcomp1, rcomp2, 0, rcompDistance-1, 0, null);
/dports/biology/bbmap/bbmap/current/aligner/
H A DAligner.java30 int[] fillAndScoreLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minScore); in fillAndScoreLimited() method
H A DMultiStateAligner9PacBioAdapter_WithBarriers.java1326 …public final int[] fillAndScoreLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, in…
1354 public final int[] fillAndScoreLimited(byte[] read, SiteScore ss, int thresh, int minScore){
1355 return fillAndScoreLimited(read, ss.chrom, ss.start, ss.stop, thresh, minScore, ss.gaps);
1655 …public final int[] fillAndScoreLimited(byte[] read, int chrom, int start, int stop, int thresh, in…
1656 …return fillAndScoreLimited(read, Data.getChromosome(chrom).array, start-thresh, stop+thresh, minSc…
H A DSingleStateAlignerPacBioAdapter.java300 …public final int[] fillAndScoreLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, in…
H A DSingleStateAlignerFlat.java414 …public final int[] fillAndScoreLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, in…
H A DSingleStateAlignerFlat2_1D.java396 …public final int[] fillAndScoreLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, in… in fillAndScoreLimited() method in SingleStateAlignerFlat2_1D
H A DSingleStateAlignerFlat2.java416 …public final int[] fillAndScoreLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, in… in fillAndScoreLimited() method in SingleStateAlignerFlat2
H A DSingleStateAlignerFlat3.java414 …public final int[] fillAndScoreLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, in… in fillAndScoreLimited() method in SingleStateAlignerFlat3
H A DSingleStateAlignerFlat2Amino.java484 …public final int[] fillAndScoreLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, in… in fillAndScoreLimited() method in SingleStateAlignerFlat2Amino
H A DSingleStateAlignerFlatFloat.java457 …public final int[] fillAndScoreLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, in… in fillAndScoreLimited() method in SingleStateAlignerFlatFloat
H A DMultiStateAligner9PacBioAdapter.java945 …public final int[] fillAndScoreLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, in…
H A DMultiStateAligner9PacBioAdapter2.java1125 …public final int[] fillAndScoreLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, in…
H A DMultiStateAligner9PacBioAdapter3.java951 …public final int[] fillAndScoreLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, in… in fillAndScoreLimited() method
/dports/biology/bbmap/bbmap/current/align2/
H A DMSA.java84 …public final int[] fillAndScoreLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, in… in fillAndScoreLimited() method in MSA
117 public final int[] fillAndScoreLimited(byte[] read, SiteScore ss, int thresh, int minScore){ in fillAndScoreLimited() method in MSA
118 return fillAndScoreLimited(read, ss.chrom, ss.start, ss.stop, thresh, minScore, ss.gaps); in fillAndScoreLimited()
123 …public final int[] fillAndScoreLimited(byte[] read, int chrom, int start, int stop, int thresh, in… in fillAndScoreLimited() method in MSA
124 …return fillAndScoreLimited(read, Data.getChromosome(chrom).array, start-thresh, stop+thresh, minSc… in fillAndScoreLimited()
H A DBBMapThread5.java303 swscoreArray=msa.fillAndScoreLimited(bases, ss, pad, minscore); in scoreSlow()
320 swscoreArray=msa.fillAndScoreLimited(bases, ss, pad, minscore); in scoreSlow()
616 …"msa unlimited return = "+Arrays.toString(msa.fillAndScoreLimited(r.strand()==Shared.PLUS ? r.base… in processRead()
618 …"msa limited return = "+Arrays.toString(msa.fillAndScoreLimited(r.strand()==Shared.PLUS ? r.bases : in processRead()
1226 Arrays.toString(msa.fillAndScoreLimited(r.strand()==Shared.PLUS ? r.bases : in processReadPair()
1228 Arrays.toString(msa.fillAndScoreLimited(r.strand()==Shared.PLUS ? r.bases : in processReadPair()
1233 Arrays.toString(msa.fillAndScoreLimited(r2.strand()==Shared.PLUS ? r2.bases : in processReadPair()
1235 Arrays.toString(msa.fillAndScoreLimited(r2.strand()==Shared.PLUS ? r2.bases : in processReadPair()
H A DBBMapThreadPacBio.java304 swscoreArray=msa.fillAndScoreLimited(bases, ss, pad, minscore); in scoreSlow()
321 swscoreArray=msa.fillAndScoreLimited(bases, ss, pad, minscore); in scoreSlow()
624 …"msa unlimited return = "+Arrays.toString(msa.fillAndScoreLimited(r.strand()==Shared.PLUS ? r.base… in processRead()
626 …"msa limited return = "+Arrays.toString(msa.fillAndScoreLimited(r.strand()==Shared.PLUS ? r.bases : in processRead()
1231 Arrays.toString(msa.fillAndScoreLimited(r.strand()==Shared.PLUS ? r.bases : in processReadPair()
1233 Arrays.toString(msa.fillAndScoreLimited(r.strand()==Shared.PLUS ? r.bases : in processReadPair()
1238 Arrays.toString(msa.fillAndScoreLimited(r2.strand()==Shared.PLUS ? r2.bases : in processReadPair()
1240 Arrays.toString(msa.fillAndScoreLimited(r2.strand()==Shared.PLUS ? r2.bases : in processReadPair()
H A DBBMapThread.java310 swscoreArray=msa.fillAndScoreLimited(bases, ss, pad, minscore); in scoreSlow()
327 swscoreArray=msa.fillAndScoreLimited(bases, ss, pad, minscore); in scoreSlow()
662 …"msa unlimited return = "+Arrays.toString(msa.fillAndScoreLimited(r.strand()==Shared.PLUS ? r.base… in processRead()
664 …"msa limited return = "+Arrays.toString(msa.fillAndScoreLimited(r.strand()==Shared.PLUS ? r.bases : in processRead()
1293 Arrays.toString(msa.fillAndScoreLimited(r.strand()==Shared.PLUS ? r.bases : in processReadPair()
1295 Arrays.toString(msa.fillAndScoreLimited(r.strand()==Shared.PLUS ? r.bases : in processReadPair()
1300 Arrays.toString(msa.fillAndScoreLimited(r2.strand()==Shared.PLUS ? r2.bases : in processReadPair()
1302 Arrays.toString(msa.fillAndScoreLimited(r2.strand()==Shared.PLUS ? r2.bases : in processReadPair()
H A DBBMapThreadAcc.java349 swscoreArray=msa.fillAndScoreLimited(bases, ss, pad, minscore); in scoreSlow()
366 swscoreArray=msa.fillAndScoreLimited(bases, ss, pad, minscore); in scoreSlow()
706 …"msa unlimited return = "+Arrays.toString(msa.fillAndScoreLimited(r.strand()==Shared.PLUS ? r.base… in processRead()
708 …"msa limited return = "+Arrays.toString(msa.fillAndScoreLimited(r.strand()==Shared.PLUS ? r.bases : in processRead()
1327 Arrays.toString(msa.fillAndScoreLimited(r.strand()==Shared.PLUS ? r.bases : in processReadPair()
1329 Arrays.toString(msa.fillAndScoreLimited(r.strand()==Shared.PLUS ? r.bases : in processReadPair()
1334 Arrays.toString(msa.fillAndScoreLimited(r2.strand()==Shared.PLUS ? r2.bases : in processReadPair()
1336 Arrays.toString(msa.fillAndScoreLimited(r2.strand()==Shared.PLUS ? r2.bases : in processReadPair()
H A DBBMapThreadPacBioSkimmer.java344 swscoreArray=msa.fillAndScoreLimited(bases, ss, pad, minscore); in scoreSlow()
361 swscoreArray=msa.fillAndScoreLimited(bases, ss, pad, minscore); in scoreSlow()
982 …"msa unlimited return = "+Arrays.toString(msa.fillAndScoreLimited(r.strand()==Shared.PLUS ? r.base… in processRead()
984 …"msa limited return = "+Arrays.toString(msa.fillAndScoreLimited(r.strand()==Shared.PLUS ? r.bases : in processRead()
1619 Arrays.toString(msa.fillAndScoreLimited(r.strand()==Shared.PLUS ? r.bases : in processReadPair()
1621 Arrays.toString(msa.fillAndScoreLimited(r.strand()==Shared.PLUS ? r.bases : in processReadPair()
1626 Arrays.toString(msa.fillAndScoreLimited(r2.strand()==Shared.PLUS ? r2.bases : in processReadPair()
1628 Arrays.toString(msa.fillAndScoreLimited(r2.strand()==Shared.PLUS ? r2.bases : in processReadPair()
H A DAbstractMapThread.java1293 …final int[] swscoreArray=msa.fillAndScoreLimited(bases, ss.chrom, ss.start(), ss.stop(), SLOW_RESC… in slowRescue()
/dports/biology/bbmap/bbmap/current/icecream/
H A DIceCreamFinder.java1058 int[] rvec=ssa.fillAndScoreLimited(adapter, array, 0, array.length, minSwScore); in alignLeftTipAdapter()
1075 int[] rvec=ssa.fillAndScoreLimited(adapter, array, 0, array.length, minSwScore);
1363 rvec=ssa.fillAndScoreLimited(adapter, array, i, j, suspectThresh); in lookForAdapter()
1376 rvec=ssa.fillAndScoreLimited(adapter, array, stop, stop+window, suspectThresh); in lookForAdapter()
1384 …rvec=msa2.fillAndScoreLimited(adapter, array, Tools.max(0, start-4), Tools.min(stop+4, array.lengt… in lookForAdapter()
1454 rvec=ssa.fillAndScoreLimited(adapter, array, i, j, suspectThresh); in trimTerminalAdapters()
1467 rvec=ssa.fillAndScoreLimited(adapter, array, stop, stop+window, suspectThresh); in trimTerminalAdapters()
1475 …rvec=msa2.fillAndScoreLimited(adapter, array, Tools.max(0, start-4), Tools.min(stop+4, array.lengt… in trimTerminalAdapters()