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Searched defs:baseChrom (Results 1 – 6 of 6) sorted by relevance

/dports/biology/bbmap/bbmap/current/align2/
H A DIndexMaker4.java354 int baseChrom=baseChrom(chrom); in fillArrays() local
441 public final int numberToChrom(int number, int baseChrom){ in numberToChrom()
454 public final int baseChrom(int chrom){return Tools.max(0, chrom&CHROM_MASK_HIGH);} in baseChrom() method in IndexMaker4.BlockMaker
H A DIndexMaker5.java351 int baseChrom=baseChrom(chrom); in fillArrays() local
438 public final int numberToChrom(int number, int baseChrom){ in numberToChrom()
451 public final int baseChrom(int chrom){return Tools.max(0, chrom&CHROM_MASK_HIGH);} in baseChrom() method in IndexMaker5.BlockMaker
H A DBBIndex.java192 assert(Solver.POINTS_PER_SITE<0) : Solver.POINTS_PER_SITE; in analyzeIndex()
1755 final int baseChrom=baseChrom(baseChrom_); in camelWalk3() local
2309 final int baseChrom=baseChrom(baseChrom_); in findMaxQscore2() local
3070 private static final int numberToChrom(int number, int baseChrom){ in numberToChrom()
3084 private static final int baseChrom(int chrom){return Tools.max(0, chrom&CHROM_MASK_HIGH);} in baseChrom() method
H A DBBIndexPacBio.java193 assert(Solver.POINTS_PER_SITE<0) : Solver.POINTS_PER_SITE; in analyzeIndex()
1683 final int baseChrom=baseChrom(baseChrom_); in findMaxQscore2() local
2345 private static final int numberToChrom(int number, int baseChrom){ in numberToChrom()
2359 public static final int baseChrom(int chrom){return Tools.max(0, chrom&CHROM_MASK_HIGH);} in baseChrom() method in BBIndexPacBio
H A DBBIndexAcc.java1800 final int baseChrom=baseChrom(baseChrom_); in findMaxQscore2() local
2546 private static final int numberToChrom(int number, int baseChrom){ in numberToChrom()
2560 private static final int baseChrom(int chrom){return Tools.max(0, chrom&CHROM_MASK_HIGH);} in baseChrom() method
H A DBBIndex5.java1722 final int baseChrom=baseChrom(baseChrom_); in findMaxQscore2() local
2362 private static final int numberToChrom(int number, int baseChrom){ in numberToChrom()
2390 private static final int baseChrom(int chrom){return Tools.max(0, chrom&CHROM_MASK_HIGH);} in baseChrom() method