/dports/biology/bbmap/bbmap/current/align2/ |
H A D | MSA.java | 152 public final int scoreNoIndels(byte[] read, SiteScore ss){ in scoreNoIndels() method in MSA 154 return scoreNoIndels(read, cha.array, ss.start); in scoreNoIndels() 157 public final int scoreNoIndels(byte[] read, final int chrom, final int refStart){ in scoreNoIndels() method in MSA 159 return scoreNoIndels(read, cha.array, refStart); in scoreNoIndels() 162 public final int scoreNoIndels(byte[] read, SiteScore ss, byte[] baseScores){ in scoreNoIndels() method in MSA 164 return scoreNoIndels(read, cha.array, baseScores, ss.start); in scoreNoIndels() 167 …public final int scoreNoIndels(byte[] read, final int chrom, final int refStart, byte[] baseScores… in scoreNoIndels() method in MSA 169 return scoreNoIndels(read, cha.array, baseScores, refStart); in scoreNoIndels() 180 public abstract int scoreNoIndels(byte[] read, byte[] ref, final int refStart); in scoreNoIndels() method in MSA 181 public int scoreNoIndels(byte[] read, byte[] ref, final int refStart, final SiteScore ss){ in scoreNoIndels() method in MSA [all …]
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H A D | MultiStateAligner11tsJNI.java | 990 public final int scoreNoIndels(byte[] read, byte[] ref, final int refStart){ 991 return scoreNoIndels(read, ref, refStart, null); 994 public final int scoreNoIndels(byte[] read, byte[] ref, final int refStart, final SiteScore ss){ 1071 public final int scoreNoIndels(byte[] read, byte[] ref, byte[] baseScores, final int refStart){ 1072 return scoreNoIndels(read, ref, baseScores, refStart, null); 1075 …public final int scoreNoIndels(byte[] read, byte[] ref, byte[] baseScores, final int refStart, Sit…
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H A D | BBMapThread5.java | 362 …assert(clipped || swscoreNoIndel==-1 || msa.scoreNoIndels(bases, ss.chrom, ss.start)==swscoreNoInd… in scoreSlow() 364 swscoreNoIndel+" != "+msa.scoreNoIndels(bases, ss.chrom, ss.start)+"\n"+ in scoreSlow() 433 int numNearPerfectScores=scoreNoIndels(r, basesP, basesM, maxSwScore, maxImperfectSwScore); in processRead() 964 int numNearPerfectScores1=scoreNoIndels(r, basesP1, basesM1, maxSwScore1, maxImperfectSwScore1); in processReadPair() 983 … int numNearPerfectScores2=scoreNoIndels(r2, basesP2, basesM2, maxSwScore2, maxImperfectSwScore2); in processReadPair()
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H A D | BBMapThreadPacBio.java | 363 …assert(clipped || swscoreNoIndel==-1 || msa.scoreNoIndels(bases, ss.chrom, ss.start)==swscoreNoInd… in scoreSlow() 365 swscoreNoIndel+" != "+msa.scoreNoIndels(bases, ss.chrom, ss.start)+"\n"+ in scoreSlow() 434 int numNearPerfectScores=scoreNoIndels(r, basesP, basesM, maxSwScore, maxImperfectSwScore); in processRead() 969 int numNearPerfectScores1=scoreNoIndels(r, basesP1, basesM1, maxSwScore1, maxImperfectSwScore1); in processReadPair() 988 … int numNearPerfectScores2=scoreNoIndels(r2, basesP2, basesM2, maxSwScore2, maxImperfectSwScore2); in processReadPair()
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H A D | BBMapThread.java | 369 …assert(clipped || swscoreNoIndel==-1 || msa.scoreNoIndels(bases, ss.chrom, ss.start)==swscoreNoInd… in scoreSlow() 371 swscoreNoIndel+" != "+msa.scoreNoIndels(bases, ss.chrom, ss.start)+"\n"+ in scoreSlow() 440 int numNearPerfectScores=scoreNoIndels(r, basesP, basesM, maxSwScore, maxImperfectSwScore); in processRead() 1031 int numNearPerfectScores1=scoreNoIndels(r, basesP1, basesM1, maxSwScore1, maxImperfectSwScore1); in processReadPair() 1050 … int numNearPerfectScores2=scoreNoIndels(r2, basesP2, basesM2, maxSwScore2, maxImperfectSwScore2); in processReadPair()
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H A D | BBMapThreadAcc.java | 408 …assert(clipped || swscoreNoIndel==-1 || msa.scoreNoIndels(bases, ss.chrom, ss.start)==swscoreNoInd… in scoreSlow() 410 swscoreNoIndel+" != "+msa.scoreNoIndels(bases, ss.chrom, ss.start)+"\n"+ in scoreSlow() 479 int numNearPerfectScores=scoreNoIndels(r, basesP, basesM, maxSwScore, maxImperfectSwScore); in processRead() 1065 int numNearPerfectScores1=scoreNoIndels(r, basesP1, basesM1, maxSwScore1, maxImperfectSwScore1); in processReadPair() 1084 … int numNearPerfectScores2=scoreNoIndels(r2, basesP2, basesM2, maxSwScore2, maxImperfectSwScore2); in processReadPair()
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H A D | MultiStateAligner11ts.java | 1929 public final int scoreNoIndels(byte[] read, byte[] ref, final int refStart){ 1930 return scoreNoIndels(read, ref, refStart, null); 1933 public final int scoreNoIndels(byte[] read, byte[] ref, final int refStart, final SiteScore ss){ 2019 public final int scoreNoIndels(byte[] read, byte[] ref, byte[] baseScores, final int refStart){ 2020 return scoreNoIndels(read, ref, baseScores, refStart, null); 2023 …public final int scoreNoIndels(byte[] read, byte[] ref, byte[] baseScores, final int refStart, Sit…
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H A D | MultiStateAligner9XFlat.java | 1778 public final int scoreNoIndels(byte[] read, byte[] ref, final int refStart){ 1779 return scoreNoIndels(read, ref, refStart, null); 1782 public final int scoreNoIndels(byte[] read, byte[] ref, final int refStart, final SiteScore ss){ 1865 public final int scoreNoIndels(byte[] read, byte[] ref, byte[] baseScores, final int refStart){ 1866 return scoreNoIndels(read, ref, baseScores, refStart, null); 1869 …public final int scoreNoIndels(byte[] read, byte[] ref, byte[] baseScores, final int refStart, Sit…
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H A D | MultiStateAligner9ts.java | 1809 public final int scoreNoIndels(byte[] read, byte[] ref, final int refStart){ 1810 return scoreNoIndels(read, ref, refStart, null); 1813 public final int scoreNoIndels(byte[] read, byte[] ref, final int refStart, final SiteScore ss){ 1898 public final int scoreNoIndels(byte[] read, byte[] ref, byte[] baseScores, final int refStart){ 1899 return scoreNoIndels(read, ref, baseScores, refStart, null); 1902 …public final int scoreNoIndels(byte[] read, byte[] ref, byte[] baseScores, final int refStart, Sit…
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H A D | MultiStateAligner9Flat.java | 1854 public final int scoreNoIndels(byte[] read, byte[] ref, final int refStart){ 1855 return scoreNoIndels(read, ref, refStart, null); 1858 public final int scoreNoIndels(byte[] read, byte[] ref, final int refStart, final SiteScore ss){ 1943 public final int scoreNoIndels(byte[] read, byte[] ref, byte[] baseScores, final int refStart){ 1944 return scoreNoIndels(read, ref, baseScores, refStart, null); 1947 …public final int scoreNoIndels(byte[] read, byte[] ref, byte[] baseScores, final int refStart, Sit…
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H A D | MultiStateAligner9PacBio.java | 1854 public final int scoreNoIndels(byte[] read, byte[] ref, final int refStart){ 1855 return scoreNoIndels(read, ref, refStart, null); 1858 public final int scoreNoIndels(byte[] read, byte[] ref, final int refStart, final SiteScore ss){ 1943 public final int scoreNoIndels(byte[] read, byte[] ref, byte[] baseScores, final int refStart){ 1944 return scoreNoIndels(read, ref, baseScores, refStart, null); 1947 …public final int scoreNoIndels(byte[] read, byte[] ref, byte[] baseScores, final int refStart, Sit…
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H A D | BBMapThreadPacBioSkimmer.java | 403 …assert(clipped || swscoreNoIndel==-1 || msa.scoreNoIndels(bases, ss.chrom, ss.start)==swscoreNoInd… in scoreSlow() 405 swscoreNoIndel+" != "+msa.scoreNoIndels(bases, ss.chrom, ss.start)+"\n"+ in scoreSlow() 783 int numNearPerfectScores=scoreNoIndels(r, basesP, basesM, maxSwScore, maxImperfectSwScore); in processRead() 1338 int numNearPerfectScores1=scoreNoIndels(r, basesP1, basesM1, maxSwScore1, maxImperfectSwScore1); in processReadPair() 1358 … int numNearPerfectScores2=scoreNoIndels(r2, basesP2, basesM2, maxSwScore2, maxImperfectSwScore2); in processReadPair()
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H A D | AbstractMapThread.java | 790 …final int scoreNoIndels(final Read r, final byte[] basesP, final byte[] basesM, final int maxSwSco… in scoreNoIndels() method in AbstractMapThread 830 …slowScoreNoIndel=msa.scoreNoIndels(bases, cha.array, ss.start(), (sslen==bases.length ? ss : null)… in scoreNoIndels() 835 int slowScoreNoIndel2=msa.scoreNoIndels(bases, cha.array, ss.stop()-bases.length+1, null); in scoreNoIndels() 1121 ss.setSlowScore(msa.scoreNoIndels(bases, ss.chrom, ss.start())); in findTipDeletions() 1277 int swscoreNoIndel=msa.scoreNoIndels(bases, ss.chrom, ss.start()); in slowRescue() 1286 swscoreNoIndel=msa.scoreNoIndels(bases, ss.chrom, ss.start()); in slowRescue()
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H A D | MultiStateAligner10ts.java | 2873 public final int scoreNoIndels(byte[] read, byte[] ref, final int refStart){ 2947 public final int scoreNoIndels(byte[] read, byte[] ref, byte[] baseScores, final int refStart){ 3154 public final int scoreNoIndels(byte[] read, byte[] ref, final int refStart, final SiteScore ss){ 3220 …public final int scoreNoIndels(byte[] read, byte[] ref, byte[] baseScores, final int refStart, Sit…
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/dports/biology/bbmap/bbmap/current/aligner/ |
H A D | MultiStateAligner9PacBioAdapter.java | 965 public final static int scoreNoIndels(byte[] read, SiteScore ss){ 967 return scoreNoIndels(read, cha.array, ss.start, ss); 970 public final static int scoreNoIndels(byte[] read, final int chrom, final int refStart){ 972 return scoreNoIndels(read, cha.array, refStart, null); 975 public final static int scoreNoIndels(byte[] read, SiteScore ss, byte[] baseScores){ 977 return scoreNoIndels(read, cha.array, baseScores, ss.start, ss); 980 …public final static int scoreNoIndels(byte[] read, final int chrom, final int refStart, byte[] bas… 982 return scoreNoIndels(read, cha.array, baseScores, refStart, null); 985 …public final static int scoreNoIndels(byte[] read, byte[] ref, final int refStart, final SiteScore… 1050 …public final static int scoreNoIndels(byte[] read, byte[] ref, byte[] baseScores, final int refSta…
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H A D | MultiStateAligner9PacBioAdapter2.java | 1146 public final static int scoreNoIndels(byte[] read, SiteScore ss){ 1148 return scoreNoIndels(read, cha.array, ss.start, ss); 1151 public final static int scoreNoIndels(byte[] read, final int chrom, final int refStart){ 1153 return scoreNoIndels(read, cha.array, refStart, null); 1156 public final static int scoreNoIndels(byte[] read, SiteScore ss, byte[] baseScores){ 1158 return scoreNoIndels(read, cha.array, baseScores, ss.start, ss); 1161 …public final static int scoreNoIndels(byte[] read, final int chrom, final int refStart, byte[] bas… 1163 return scoreNoIndels(read, cha.array, baseScores, refStart, null); 1168 …public final static int scoreNoIndels(byte[] read, byte[] ref, final int refStart, final SiteScore… 1233 …public final static int scoreNoIndels(byte[] read, byte[] ref, byte[] baseScores, final int refSta…
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H A D | MultiStateAligner9PacBioAdapter3.java | 971 public final static int scoreNoIndels(byte[] read, SiteScore ss){ in scoreNoIndels() method 973 return scoreNoIndels(read, cha.array, ss.start, ss); in scoreNoIndels() 976 public final static int scoreNoIndels(byte[] read, final int chrom, final int refStart){ in scoreNoIndels() method 978 return scoreNoIndels(read, cha.array, refStart, null); in scoreNoIndels() 981 public final static int scoreNoIndels(byte[] read, SiteScore ss, byte[] baseScores){ in scoreNoIndels() method 983 return scoreNoIndels(read, cha.array, baseScores, ss.start, ss); in scoreNoIndels() 986 …public final static int scoreNoIndels(byte[] read, final int chrom, final int refStart, byte[] bas… in scoreNoIndels() method 988 return scoreNoIndels(read, cha.array, baseScores, refStart, null); in scoreNoIndels() 991 …public final static int scoreNoIndels(byte[] read, byte[] ref, final int refStart, final SiteScore… in scoreNoIndels() method 1056 …public final static int scoreNoIndels(byte[] read, byte[] ref, byte[] baseScores, final int refSta… in scoreNoIndels() method
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H A D | MultiStateAligner9PacBioAdapter_WithBarriers.java | 1725 public final static int scoreNoIndels(byte[] read, SiteScore ss){ 1727 return scoreNoIndels(read, cha.array, ss.start, ss); 1730 public final static int scoreNoIndels(byte[] read, final int chrom, final int refStart){ 1732 return scoreNoIndels(read, cha.array, refStart, null); 1735 public final static int scoreNoIndels(byte[] read, SiteScore ss, byte[] baseScores){ 1737 return scoreNoIndels(read, cha.array, baseScores, ss.start, ss); 1740 …public final static int scoreNoIndels(byte[] read, final int chrom, final int refStart, byte[] bas… 1742 return scoreNoIndels(read, cha.array, baseScores, refStart, null); 1970 …public final static int scoreNoIndels(byte[] read, byte[] ref, final int refStart, final SiteScore… 2035 …public final static int scoreNoIndels(byte[] read, byte[] ref, byte[] baseScores, final int refSta…
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