/dports/biology/bbmap/bbmap/current/pacbio/ |
H A D | RemoveAdapters2.java | 438 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…
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H A D | RemoveAdapters3.java | 394 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);
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/dports/biology/bbmap/bbmap/current/aligner/ |
H A D | Aligner.java | 30 int[] fillAndScoreLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minScore); in fillAndScoreLimited() method
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H A D | MultiStateAligner9PacBioAdapter_WithBarriers.java | 1326 …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…
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H A D | SingleStateAlignerPacBioAdapter.java | 300 …public final int[] fillAndScoreLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, in…
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H A D | SingleStateAlignerFlat.java | 414 …public final int[] fillAndScoreLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, in…
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H A D | SingleStateAlignerFlat2_1D.java | 396 …public final int[] fillAndScoreLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, in… in fillAndScoreLimited() method in SingleStateAlignerFlat2_1D
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H A D | SingleStateAlignerFlat2.java | 416 …public final int[] fillAndScoreLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, in… in fillAndScoreLimited() method in SingleStateAlignerFlat2
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H A D | SingleStateAlignerFlat3.java | 414 …public final int[] fillAndScoreLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, in… in fillAndScoreLimited() method in SingleStateAlignerFlat3
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H A D | SingleStateAlignerFlat2Amino.java | 484 …public final int[] fillAndScoreLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, in… in fillAndScoreLimited() method in SingleStateAlignerFlat2Amino
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H A D | SingleStateAlignerFlatFloat.java | 457 …public final int[] fillAndScoreLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, in… in fillAndScoreLimited() method in SingleStateAlignerFlatFloat
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H A D | MultiStateAligner9PacBioAdapter.java | 945 …public final int[] fillAndScoreLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, in…
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H A D | MultiStateAligner9PacBioAdapter2.java | 1125 …public final int[] fillAndScoreLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, in…
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H A D | MultiStateAligner9PacBioAdapter3.java | 951 …public final int[] fillAndScoreLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, in… in fillAndScoreLimited() method
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/dports/biology/bbmap/bbmap/current/align2/ |
H A D | MSA.java | 84 …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()
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H A D | BBMapThread5.java | 303 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()
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H A D | BBMapThreadPacBio.java | 304 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()
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H A D | BBMapThread.java | 310 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()
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H A D | BBMapThreadAcc.java | 349 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()
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H A D | BBMapThreadPacBioSkimmer.java | 344 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()
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H A D | AbstractMapThread.java | 1293 …final int[] swscoreArray=msa.fillAndScoreLimited(bases, ss.chrom, ss.start(), ss.stop(), SLOW_RESC… in slowRescue()
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/dports/biology/bbmap/bbmap/current/icecream/ |
H A D | IceCreamFinder.java | 1058 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()
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