Searched defs:scoreNoIndels (Results 1 – 3 of 3) sorted by relevance
| /dports/biology/bbmap/bbmap/current/aligner/ |
| H A D | MultiStateAligner9PacBioAdapter3.java | 971 public final static int scoreNoIndels(byte[] read, SiteScore ss){ in scoreNoIndels() method
976 public final static int scoreNoIndels(byte[] read, final int chrom, final int refStart){ in scoreNoIndels() method
981 public final static int scoreNoIndels(byte[] read, SiteScore ss, byte[] baseScores){ in scoreNoIndels() method
986 …public final static int scoreNoIndels(byte[] read, final int chrom, final int refStart, byte[] bas… in scoreNoIndels() method
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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| /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
157 public final int scoreNoIndels(byte[] read, final int chrom, final int refStart){ in scoreNoIndels() method in MSA
162 public final int scoreNoIndels(byte[] read, SiteScore ss, byte[] baseScores){ in scoreNoIndels() method in MSA
167 …public final int scoreNoIndels(byte[] read, final int chrom, final int refStart, byte[] baseScores… in scoreNoIndels() method in MSA
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
187 public abstract int scoreNoIndels(byte[] read, byte[] ref, byte[] baseScores, final int refStart); in scoreNoIndels() method in MSA
188 …public int scoreNoIndels(byte[] read, byte[] ref, byte[] baseScores, final int refStart, SiteScore… in scoreNoIndels() method in MSA
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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
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