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Searched refs:baseScores (Results 1 – 18 of 18) sorted by relevance

/dports/biology/bbmap/bbmap/current/align2/
H A DMSA.java136 int[] max=fillQ(read, ref, baseScores, a, b); in fillAndScoreQ()
143 public final int[] fillAndScoreQ(byte[] read, SiteScore ss, int thresh, byte[] baseScores){ in fillAndScoreQ() argument
144 return fillAndScoreQ(read, ss.chrom, ss.start, ss.stop, thresh, baseScores); in fillAndScoreQ()
149 …return fillAndScoreQ(read, Data.getChromosome(chrom).array, start-thresh, stop+thresh, baseScores); in fillAndScoreQ()
162 public final int scoreNoIndels(byte[] read, SiteScore ss, byte[] baseScores){ in scoreNoIndels() argument
164 return scoreNoIndels(read, cha.array, baseScores, ss.start); in scoreNoIndels()
169 return scoreNoIndels(read, cha.array, baseScores, refStart); in scoreNoIndels()
175 public abstract int calcAffineScore(int[] locArray, byte[] baseScores, byte[] bases); in calcAffineScore() argument
187 public abstract int scoreNoIndels(byte[] read, byte[] ref, byte[] baseScores, final int refStart); in scoreNoIndels() argument
548 public abstract int maxQuality(byte[] baseScores); in maxQuality() argument
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H A DMultiStateAligner11tsJNI.java842 score+=(POINTS_MATCH2+baseScores[i]);
844 score+=(POINTS_MATCH+baseScores[i]);
847 score+=(POINTS_MATCH+baseScores[i]);
922 score+=(POINTS_MATCH2+baseScores[i]);
926 score+=(POINTS_MATCH+baseScores[i]);
931 score+=(POINTS_MATCH+baseScores[i]);
1112 score+=baseScores[i];
1182 score+=baseScores[i];
1286 public final int maxQuality(byte[] baseScores){
1287 return POINTS_MATCH+(baseScores.length-1)*(POINTS_MATCH2)+Tools.sumInt(baseScores);
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H A DMultiStateAligner11ts.java1747 score+=(POINTS_MATCH2+baseScores[i]);
1749 score+=(POINTS_MATCH+baseScores[i]);
1752 score+=(POINTS_MATCH+baseScores[i]);
1844 score+=(POINTS_MATCH2+baseScores[i]);
1848 score+=(POINTS_MATCH+baseScores[i]);
1853 score+=(POINTS_MATCH+baseScores[i]);
2063 score+=baseScores[i];
2142 score+=baseScores[i];
2253 public final int maxQuality(byte[] baseScores){
2254 return POINTS_MATCH+(baseScores.length-1)*(POINTS_MATCH2)+Tools.sumInt(baseScores);
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H A DMultiStateAligner9XFlat.java1638 score+=(POINTS_MATCH2+baseScores[i]);
1640 score+=(POINTS_MATCH+baseScores[i]);
1643 score+=(POINTS_MATCH+baseScores[i]);
1657 score+=(POINTS_MATCH+baseScores[i]);
1718 score+=(POINTS_MATCH+baseScores[i]);
1723 score+=(POINTS_MATCH+baseScores[i]);
1739 score+=(POINTS_MATCH+baseScores[i]);
1909 score+=baseScores[i];
1985 score+=baseScores[i];
2088 return POINTS_MATCH+(baseScores.length-1)*(POINTS_MATCH2)+Tools.sumInt(baseScores);
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H A DMultiStateAligner9ts.java1629 score+=(POINTS_MATCH2+baseScores[i]);
1631 score+=(POINTS_MATCH+baseScores[i]);
1634 score+=(POINTS_MATCH+baseScores[i]);
1664 score+=(POINTS_MATCH+baseScores[i]);
1729 score+=(POINTS_MATCH+baseScores[i]);
1734 score+=(POINTS_MATCH+baseScores[i]);
1766 score+=(POINTS_MATCH+baseScores[i]);
1942 score+=baseScores[i];
2020 score+=baseScores[i];
2127 return POINTS_MATCH+(baseScores.length-1)*(POINTS_MATCH2)+Tools.sumInt(baseScores);
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H A DMultiStateAligner9Flat.java1674 score+=(POINTS_MATCH2+baseScores[i]);
1676 score+=(POINTS_MATCH+baseScores[i]);
1679 score+=(POINTS_MATCH+baseScores[i]);
1709 score+=(POINTS_MATCH+baseScores[i]);
1774 score+=(POINTS_MATCH+baseScores[i]);
1779 score+=(POINTS_MATCH+baseScores[i]);
1811 score+=(POINTS_MATCH+baseScores[i]);
1987 score+=baseScores[i];
2065 score+=baseScores[i];
2172 return POINTS_MATCH+(baseScores.length-1)*(POINTS_MATCH2)+Tools.sumInt(baseScores);
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H A DMultiStateAligner9PacBio.java1674 score+=(POINTS_MATCH2+baseScores[i]);
1676 score+=(POINTS_MATCH+baseScores[i]);
1679 score+=(POINTS_MATCH+baseScores[i]);
1709 score+=(POINTS_MATCH+baseScores[i]);
1774 score+=(POINTS_MATCH+baseScores[i]);
1779 score+=(POINTS_MATCH+baseScores[i]);
1811 score+=(POINTS_MATCH+baseScores[i]);
1987 score+=baseScores[i];
2065 score+=baseScores[i];
2172 return POINTS_MATCH+(baseScores.length-1)*(POINTS_MATCH2)+Tools.sumInt(baseScores);
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H A DMultiStateAligner10ts.java2697 score+=(POINTS_MATCH+baseScores[i]);
2700 score+=(POINTS_MATCH+baseScores[i]);
2730 score+=(POINTS_MATCH+baseScores[i]);
2793 score+=(POINTS_MATCH+baseScores[i]);
2798 score+=(POINTS_MATCH+baseScores[i]);
2830 score+=(POINTS_MATCH+baseScores[i]);
2982 score+=baseScores[i];
3053 score+=baseScores[i];
3260 score+=baseScores[i];
3294 return POINTS_MATCH+(baseScores.length-1)*(POINTS_MATCH2)+Tools.sumInt(baseScores);
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H A DBBIndex5.java813 final byte[] baseScores, int[] keyScores, int[] offsets,
853 final int maxScore=maxScore(offsets, baseScores, keyScores, bases.length, true);
953 …score=extendScore(bases, baseScores, offsets, values, chrom, centerIndex, locArray, numHits, appro…
1236 final byte[] baseScores, int[] keyScores, int[] offsets,
1406 …score=extendScore(bases, baseScores, offsets, values, chrom, centerIndex, locArray, numHits, appro…
1883 …final int maxScore(int[] offsets, byte[] baseScores, int[] keyScores, int readlen, boolean useQual… in maxScore() argument
1887 if(USE_AFFINE_SCORE){return msa.maxQuality(baseScores);} in maxScore()
1888 … if(USE_EXTENDED_SCORE){return readlen*(BASE_HIT_SCORE+BASE_HIT_SCORE/5)+Tools.sumInt(baseScores);} in maxScore()
2117 int score=(KFILTER<2 ? msa.calcAffineScore(locArray, baseScores, bases) : in extendScore()
2118 msa.calcAffineScore(locArray, baseScores, bases, KFILTER)); in extendScore()
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H A DBBIndexPacBio.java820 final byte[] baseScores, int[] keyScores, int[] offsets,
859 final int maxScore=maxScore(offsets, baseScores, keyScores, bases.length, true);
960 …score=extendScore(bases, baseScores, offsets, values, chrom, centerIndex, locArray, numHits, appro…
1220 final byte[] baseScores, int[] keyScores, int[] offsets,
1385 …score=extendScore(bases, baseScores, offsets, values, chrom, centerIndex, locArray, numHits, appro…
1843 …final int maxScore(int[] offsets, byte[] baseScores, int[] keyScores, int readlen, boolean useQual… in maxScore() argument
1847 if(USE_AFFINE_SCORE){return msa.maxQuality(baseScores);} in maxScore()
1848 … if(USE_EXTENDED_SCORE){return readlen*(BASE_HIT_SCORE+BASE_HIT_SCORE/5)+Tools.sumInt(baseScores);} in maxScore()
2105 int score=(KFILTER<2 ? msa.calcAffineScore(locArray, baseScores, bases) : in extendScore()
2106 msa.calcAffineScore(locArray, baseScores, bases, KFILTER)); in extendScore()
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H A DBBIndex.java858 final byte[] baseScores, int[] keyScores, int[] offsets,
879 final int maxScore=maxScore(offsets, baseScores, keyScores, bases.length, true);
977 …score=extendScore(bases, baseScores, offsets, values, chrom, centerIndex, locArray, numHits, appro…
1224 final byte[] baseScores, int[] keyScores, int[] offsets,
1717 final byte[] baseScores, int[] keyScores, int[] offsets, in camelWalk3() argument
2469 …final int maxScore(int[] offsets, byte[] baseScores, int[] keyScores, int readlen, boolean useQual… in maxScore() argument
2473 if(USE_AFFINE_SCORE){return msa.maxQuality(baseScores);} in maxScore()
2474 … if(USE_EXTENDED_SCORE){return readlen*(BASE_HIT_SCORE+BASE_HIT_SCORE/5)+Tools.sumInt(baseScores);} in maxScore()
2830 int score=(KFILTER<2 ? msa.calcAffineScore(locArray, baseScores, bases) : in extendScore()
2831 msa.calcAffineScore(locArray, baseScores, bases, KFILTER)); in extendScore()
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H A DBBIndexAcc.java920 final byte[] baseScores, int[] keyScores, int[] offsets,
941 final int maxScore=maxScore(offsets, baseScores, keyScores, bases.length, true);
1043 …score=extendScore(bases, baseScores, offsets, values, chrom, centerIndex, locArray, numHits, appro…
1304 final byte[] baseScores, int[] keyScores, int[] offsets,
1470 …score=extendScore(bases, baseScores, offsets, values, chrom, centerIndex, locArray, numHits, appro…
1958 …final int maxScore(int[] offsets, byte[] baseScores, int[] keyScores, int readlen, boolean useQual… in maxScore() argument
1962 if(USE_AFFINE_SCORE){return msa.maxQuality(baseScores);} in maxScore()
1963 … if(USE_EXTENDED_SCORE){return readlen*(BASE_HIT_SCORE+BASE_HIT_SCORE/5)+Tools.sumInt(baseScores);} in maxScore()
2306 int score=(KFILTER<2 ? msa.calcAffineScore(locArray, baseScores, bases) : in extendScore()
2307 msa.calcAffineScore(locArray, baseScores, bases, KFILTER)); in extendScore()
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H A DBBIndexPacBioSkimmer.java798 …public final ArrayList<SiteScore> find(int[] keys, final byte[] bases, final byte[] baseScores, in…
813 …ssl=slowWalk3(starts, stops, bases, baseScores, keyScores, offsets, chrom, strand, obeyLimits, ssl…
893 final byte[] baseScores, int[] keyScores, int[] offsets,
1055 …score=extendScore(bases, baseScores, offsets, values, chrom, centerIndex, locArray, numHits, appro…
1506 …final int maxScore(int[] offsets, byte[] baseScores, int[] keyScores, int readlen, boolean useQual…
1510 if(USE_AFFINE_SCORE){return msa.maxQuality(baseScores);}
1511 … if(USE_EXTENDED_SCORE){return readlen*(BASE_HIT_SCORE+BASE_HIT_SCORE/5)+Tools.sumInt(baseScores);}
1640 …private final int extendScore(final byte[] bases, final byte[] baseScores, final int[] offsets, fi…
1775 int score=(KFILTER<2 ? msa.calcAffineScore(locArray, baseScores, bases) :
1776 msa.calcAffineScore(locArray, baseScores, bases, KFILTER));
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H A DAbstractIndex.java83 …abstract int maxScore(int[] offsets, byte[] baseScores, int[] keyScores, int readlen, boolean useQ… in maxScore() argument
/dports/biology/bbmap/bbmap/current/aligner/
H A DMultiStateAligner9PacBioAdapter_WithBarriers.java1668 int[] max=fillQ(read, ref, baseScores, a, b);
1898 score+=(POINTS_MATCH2+baseScores[i]);
1900 score+=(POINTS_MATCH+baseScores[i]);
1903 score+=(POINTS_MATCH+baseScores[i]);
1933 score+=(POINTS_MATCH+baseScores[i]);
2075 score+=baseScores[i];
2151 score+=baseScores[i];
2254 public static final int maxQuality(byte[] baseScores){
2255 return POINTS_MATCH+(baseScores.length-1)*(POINTS_MATCH2)+Tools.sumInt(baseScores);
2271 public static final int maxImperfectScore(byte[] baseScores){
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H A DMultiStateAligner9PacBioAdapter.java975 public final static int scoreNoIndels(byte[] read, SiteScore ss, byte[] baseScores){
977 return scoreNoIndels(read, cha.array, baseScores, ss.start, ss);
980 …inal static int scoreNoIndels(byte[] read, final int chrom, final int refStart, byte[] baseScores){
982 return scoreNoIndels(read, cha.array, baseScores, refStart, null);
1050 …public final static int scoreNoIndels(byte[] read, byte[] ref, byte[] baseScores, final int refSta…
1090 score+=baseScores[i];
1166 score+=baseScores[i];
1269 public static final int maxQuality(byte[] baseScores){
1270 return POINTS_MATCH+(baseScores.length-1)*(POINTS_MATCH2)+Tools.sumInt(baseScores);
1286 public static final int maxImperfectScore(byte[] baseScores){
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H A DMultiStateAligner9PacBioAdapter2.java1156 public final static int scoreNoIndels(byte[] read, SiteScore ss, byte[] baseScores){
1158 return scoreNoIndels(read, cha.array, baseScores, ss.start, ss);
1161 …inal static int scoreNoIndels(byte[] read, final int chrom, final int refStart, byte[] baseScores){
1163 return scoreNoIndels(read, cha.array, baseScores, refStart, null);
1233 …public final static int scoreNoIndels(byte[] read, byte[] ref, byte[] baseScores, final int refSta…
1273 score+=baseScores[i];
1349 score+=baseScores[i];
1452 public static final int maxQuality(byte[] baseScores){
1453 return POINTS_MATCH+(baseScores.length-1)*(POINTS_MATCH2)+Tools.sumInt(baseScores);
1469 public static final int maxImperfectScore(byte[] baseScores){
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H A DMultiStateAligner9PacBioAdapter3.java981 public final static int scoreNoIndels(byte[] read, SiteScore ss, byte[] baseScores){ in scoreNoIndels() argument
983 return scoreNoIndels(read, cha.array, baseScores, ss.start, ss); in scoreNoIndels()
986 …inal static int scoreNoIndels(byte[] read, final int chrom, final int refStart, byte[] baseScores){ in scoreNoIndels() argument
988 return scoreNoIndels(read, cha.array, baseScores, refStart, null); in scoreNoIndels()
1056 …public final static int scoreNoIndels(byte[] read, byte[] ref, byte[] baseScores, final int refSta… in scoreNoIndels() argument
1096 score+=baseScores[i]; in scoreNoIndels()
1172 score+=baseScores[i]; in scoreNoIndelsAndMakeMatchString()
1275 public static final int maxQuality(byte[] baseScores){ in maxQuality() argument
1276 return POINTS_MATCH+(baseScores.length-1)*(POINTS_MATCH2)+Tools.sumInt(baseScores); in maxQuality()
1292 public static final int maxImperfectScore(byte[] baseScores){
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