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

/dports/biology/bbmap/bbmap/current/align2/
H A DMSA.java152 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 …]
H A DMultiStateAligner11tsJNI.java990 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…
H A DBBMapThread5.java362 …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()
H A DBBMapThreadPacBio.java363 …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()
H A DBBMapThread.java369 …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()
H A DBBMapThreadAcc.java408 …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()
H A DMultiStateAligner11ts.java1929 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…
H A DMultiStateAligner9XFlat.java1778 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…
H A DMultiStateAligner9ts.java1809 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…
H A DMultiStateAligner9Flat.java1854 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…
H A DMultiStateAligner9PacBio.java1854 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…
H A DBBMapThreadPacBioSkimmer.java403 …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()
H A DAbstractMapThread.java790 …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()
H A DMultiStateAligner10ts.java2873 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…
/dports/biology/bbmap/bbmap/current/aligner/
H A DMultiStateAligner9PacBioAdapter.java965 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…
H A DMultiStateAligner9PacBioAdapter2.java1146 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…
H A DMultiStateAligner9PacBioAdapter3.java971 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
H A DMultiStateAligner9PacBioAdapter_WithBarriers.java1725 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…