/dports/biology/bbmap/bbmap/current/align2/ |
H A D | MSA.java | 136 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 [all …]
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H A D | MultiStateAligner11tsJNI.java | 842 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); [all …]
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H A D | MultiStateAligner11ts.java | 1747 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); [all …]
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H A D | MultiStateAligner9XFlat.java | 1638 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); [all …]
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H A D | MultiStateAligner9ts.java | 1629 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); [all …]
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H A D | MultiStateAligner9Flat.java | 1674 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); [all …]
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H A D | MultiStateAligner9PacBio.java | 1674 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); [all …]
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H A D | MultiStateAligner10ts.java | 2697 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); [all …]
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H A D | BBIndex5.java | 813 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() [all …]
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H A D | BBIndexPacBio.java | 820 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() [all …]
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H A D | BBIndex.java | 858 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() [all …]
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H A D | BBIndexAcc.java | 920 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() [all …]
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H A D | BBIndexPacBioSkimmer.java | 798 …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)); [all …]
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H A D | AbstractIndex.java | 83 …abstract int maxScore(int[] offsets, byte[] baseScores, int[] keyScores, int readlen, boolean useQ… in maxScore() argument
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/dports/biology/bbmap/bbmap/current/aligner/ |
H A D | MultiStateAligner9PacBioAdapter_WithBarriers.java | 1668 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){ [all …]
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H A D | MultiStateAligner9PacBioAdapter.java | 975 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){ [all …]
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H A D | MultiStateAligner9PacBioAdapter2.java | 1156 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){ [all …]
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H A D | MultiStateAligner9PacBioAdapter3.java | 981 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){ [all …]
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