Searched defs:basesP (Results 1 – 10 of 10) sorted by relevance
| /dports/biology/bbmap/bbmap/current/align2/ |
| H A D | AbstractMapThread.java | 790 …final int scoreNoIndels(final Read r, final byte[] basesP, final byte[] basesM, final int maxSwSco… in scoreNoIndels()
888 …public final void genMatchString(final Read r, final byte[] basesP, final byte[] basesM, final int… in genMatchString()
996 …protected final int genMatchStringForSite(final long id, final SiteScore ss, final byte[] basesP, … in genMatchStringForSite()
1103 …final void findTipDeletions(final Read r, final byte[] basesP, final byte[] basesM, final int maxS… in findTipDeletions()
1172 final void rescue(Read anchor, Read loose, byte[] basesP, byte[] basesM, int searchDist){ in rescue()
1448 …public abstract void scoreSlow(final ArrayList<SiteScore> list, final byte[] basesP, final byte[] … in scoreSlow()
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| H A D | AbstractIndex.java | 84 …public abstract ArrayList<SiteScore> findAdvanced(byte[] basesP, byte[] basesM, byte[] qual, byte[… in findAdvanced()
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| H A D | BBMapThread5.java | 246 public void scoreSlow(final ArrayList<SiteScore> list, final byte[] basesP, final byte[] basesM, in scoreSlow()
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| H A D | BBMapThreadPacBio.java | 247 public void scoreSlow(final ArrayList<SiteScore> list, final byte[] basesP, final byte[] basesM, in scoreSlow()
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| H A D | BBMapThread.java | 253 public void scoreSlow(final ArrayList<SiteScore> list, final byte[] basesP, final byte[] basesM, in scoreSlow()
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| H A D | BBMapThreadAcc.java | 292 public void scoreSlow(final ArrayList<SiteScore> list, final byte[] basesP, final byte[] basesM, in scoreSlow()
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| H A D | BBIndexPacBio.java | 193 assert(Solver.POINTS_PER_SITE<0) : Solver.POINTS_PER_SITE; in analyzeIndex()
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| H A D | BBMapThreadPacBioSkimmer.java | 287 public void scoreSlow(final ArrayList<SiteScore> list, final byte[] basesP, final byte[] basesM, in scoreSlow()
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| H A D | BBIndex.java | 192 assert(Solver.POINTS_PER_SITE<0) : Solver.POINTS_PER_SITE; in analyzeIndex()
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| /dports/biology/bbmap/bbmap/current/stream/ |
| H A D | Read.java | 3685 …public static final boolean CHECKSITES(ArrayList<SiteScore> list, byte[] basesP, byte[] basesM, lo… in CHECKSITES()
3689 …public static final boolean CHECKSITES(ArrayList<SiteScore> list, byte[] basesP, byte[] basesM, lo… in CHECKSITES()
3727 public static final boolean CHECKSITE(SiteScore ss, byte[] basesP, byte[] basesM, long id){ in CHECKSITE()
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