/dports/biology/bbmap/bbmap/current/aligner/ |
H A D | MultiStateAligner9PacBioAdapter.java | 45 Arrays.fill(vertLimit, BADoff); in MultiStateAligner9PacBioAdapter() 46 Arrays.fill(horizLimit, BADoff); in MultiStateAligner9PacBioAdapter() 55 packed[matrix][i][j]|=BADoff; in MultiStateAligner9PacBioAdapter() 120 Arrays.fill(packed[x][rows], 1, columns+1, BADoff); in fillLimitedX() 134 assert(subfloor>BADoff); //TODO: Actually, it needs to be substantially more. in fillLimitedX() 135 assert(subfloor<minScore_off) : minScore_off+", "+floor+", "+BADoff+", "+subfloor; in fillLimitedX() 143 System.out.println("BADoff="+(BADoff>>SCOREOFFSET)+"\t"+(BADoff)); in fillLimitedX() 383 assert(score>=MINoff_SCORE || score==BADoff) : "Score overflow - use MSA2 instead"; in fillLimitedX() 479 assert(maxScore>=BADoff); in fillLimitedX() 505 assert(subfloor>BADoff && subfloor*2>BADoff); //TODO: Actually, it needs to be substantially more. in fillUnlimited() [all …]
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H A D | MultiStateAligner9PacBioAdapter2.java | 107 Arrays.fill(vertLimit, BADoff); in initialize() 108 Arrays.fill(horizLimit, BADoff); in initialize() 113 packed[matrix][i][j]|=BADoff; in initialize() 176 Arrays.fill(packed[x][rows], 1, columns+1, BADoff); in fillLimitedX() 190 assert(subfloor>BADoff); //TODO: Actually, it needs to be substantially more. in fillLimitedX() 191 assert(subfloor<minScore_off) : minScore_off+", "+floor+", "+BADoff+", "+subfloor; in fillLimitedX() 199 System.out.println("BADoff="+(BADoff>>SCOREOFFSET)+"\t"+(BADoff)); in fillLimitedX() 450 assert(score>=MINoff_SCORE || score==BADoff) : "Score overflow - use MSA2 instead"; in fillLimitedX() 548 assert(maxScore>=BADoff); in fillLimitedX() 577 …assert(subfloor>BADoff && subfloor*2>BADoff) : subfloor+", "+BADoff+", "+read.length; //TODO: Actu… in fillUnlimited() [all …]
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H A D | MultiStateAligner9PacBioAdapter3.java | 56 Arrays.fill(vertLimit, BADoff); in MultiStateAligner9PacBioAdapter3() 57 Arrays.fill(horizLimit, BADoff); in MultiStateAligner9PacBioAdapter3() 62 packed[matrix][i][j]|=BADoff; in MultiStateAligner9PacBioAdapter3() 116 Arrays.fill(packed[x][rows], 1, columns+1, BADoff); in fillLimitedX() 130 assert(subfloor>BADoff); //TODO: Actually, it needs to be substantially more. in fillLimitedX() 131 assert(subfloor<minScore_off) : minScore_off+", "+floor+", "+BADoff+", "+subfloor; in fillLimitedX() 139 System.out.println("BADoff="+(BADoff>>SCOREOFFSET)+"\t"+(BADoff)); in fillLimitedX() 376 assert(score>=MINoff_SCORE || score==BADoff) : "Score overflow - use MSA2 instead"; in fillLimitedX() 472 assert(maxScore>=BADoff); in fillLimitedX() 498 assert(subfloor>BADoff && subfloor*2>BADoff); //TODO: Actually, it needs to be substantially more. in fillUnlimited() [all …]
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H A D | SingleStateAlignerPacBioAdapter.java | 37 Arrays.fill(vertLimit, BADoff); in SingleStateAlignerPacBioAdapter() 38 Arrays.fill(horizLimit, BADoff); in SingleStateAlignerPacBioAdapter() 46 packed[i][j]|=BADoff; in SingleStateAlignerPacBioAdapter() 436 public static final int BADoff=(BAD<<SCOREOFFSET);
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H A D | MultiStateAligner9PacBioAdapter_WithBarriers.java | 76 Arrays.fill(vertLimit, BADoff); in MultiStateAligner9PacBioAdapter_WithBarriers() 77 Arrays.fill(horizLimit, BADoff); in MultiStateAligner9PacBioAdapter_WithBarriers() 86 packed[matrix][i][j]|=BADoff; in MultiStateAligner9PacBioAdapter_WithBarriers() 161 Arrays.fill(packed[x][rows], 1, columns+1, BADoff); in fillLimitedX() 175 assert(subfloor>BADoff); //TODO: Actually, it needs to be substantially more. in fillLimitedX() 176 assert(subfloor<minScore_off) : minScore_off+", "+floor+", "+BADoff+", "+subfloor; in fillLimitedX() 184 System.out.println("BADoff="+(BADoff>>SCOREOFFSET)+"\t"+(BADoff)); in fillLimitedX() 443 assert(score>=MINoff_SCORE || score==BADoff) : "Score overflow - use MSA2 instead"; in fillLimitedX() 542 assert(maxScore>=BADoff); in fillLimitedX() 580 assert(subfloor>BADoff && subfloor*2>BADoff); //TODO: Actually, it needs to be substantially more. in fillUnlimited() [all …]
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H A D | SingleStateAlignerFlat.java | 528 public static final int BADoff=(BAD<<SCOREOFFSET);
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/dports/biology/bbmap/bbmap/current/align2/ |
H A D | MultiStateAligner10ts.java | 59 Arrays.fill(vertLimit, BADoff); in MultiStateAligner10ts() 60 Arrays.fill(horizLimit, BADoff); in MultiStateAligner10ts() 65 packed[matrix][i][j]|=BADoff; in MultiStateAligner10ts() 162 Arrays.fill(packed[x][rows], 1, columns+1, BADoff); in fillLimitedX() 185 System.out.println("BADoff="+(BADoff>>SCOREOFFSET)+"\t"+(BADoff)); in fillLimitedX() 569 assert(maxScore>=BADoff); in fillLimitedX() 660 System.out.println("BADoff="+(BADoff>>SCOREOFFSET)+"\t"+(BADoff)); in fillBanded1() 1044 assert(maxScore>=BADoff); in fillBanded1() 1112 System.out.println("BADoff="+(BADoff>>SCOREOFFSET)+"\t"+(BADoff)); 1518 assert(maxScore>=BADoff); [all …]
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H A D | MultiStateAligner11ts.java | 58 Arrays.fill(vertLimit, BADoff); in MultiStateAligner11ts() 59 Arrays.fill(horizLimit, BADoff); in MultiStateAligner11ts() 68 packed[matrix][i][j]|=BADoff; in MultiStateAligner11ts() 149 Arrays.fill(packed[x][y], 1, columns+1, BADoff); in fillLimitedX() 157 Arrays.fill(packed[x][rows], 1, columns+1, BADoff); in fillLimitedX() 171 assert(subfloor>BADoff); //TODO: Actually, it needs to be substantially more. in fillLimitedX() 172 assert(subfloor<minScore_off) : minScore_off+", "+floor+", "+BADoff+", "+subfloor; in fillLimitedX() 180 System.out.println("BADoff="+(BADoff>>SCOREOFFSET)+"\t"+(BADoff)); in fillLimitedX() 566 assert(maxScore>=BADoff); in fillLimitedX() 644 …assert(subfloor>BADoff && subfloor*2L>BADoff) : (read.length-1)+", "+maxGain+", "+subfloor+", "+(s… in fillUnlimited() [all …]
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H A D | MultiStateAligner9XFlat.java | 54 Arrays.fill(vertLimit, BADoff); in MultiStateAligner9XFlat() 55 Arrays.fill(horizLimit, BADoff); in MultiStateAligner9XFlat() 64 packed[matrix][i][j]|=BADoff; in MultiStateAligner9XFlat() 145 Arrays.fill(packed[x][y], 1, columns+1, BADoff); in fillLimitedX() 153 Arrays.fill(packed[x][rows], 1, columns+1, BADoff); in fillLimitedX() 167 assert(subfloor>BADoff); //TODO: Actually, it needs to be substantially more. in fillLimitedX() 168 assert(subfloor<minScore_off) : minScore_off+", "+floor+", "+BADoff+", "+subfloor; in fillLimitedX() 176 System.out.println("BADoff="+(BADoff>>SCOREOFFSET)+"\t"+(BADoff)); in fillLimitedX() 555 assert(maxScore>=BADoff); in fillLimitedX() 602 …assert(subfloor>BADoff && subfloor*2>BADoff) : (read.length-1)+", "+maxGain+", "+subfloor+", "+(su… in fillUnlimited() [all …]
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H A D | MultiStateAligner9ts.java | 57 Arrays.fill(vertLimit, BADoff); in MultiStateAligner9ts() 58 Arrays.fill(horizLimit, BADoff); in MultiStateAligner9ts() 67 packed[matrix][i][j]|=BADoff; in MultiStateAligner9ts() 145 Arrays.fill(packed[x][rows], 1, columns+1, BADoff); in fillLimitedX() 159 assert(subfloor>BADoff); //TODO: Actually, it needs to be substantially more. in fillLimitedX() 160 assert(subfloor<minScore_off) : minScore_off+", "+floor+", "+BADoff+", "+subfloor; in fillLimitedX() 168 System.out.println("BADoff="+(BADoff>>SCOREOFFSET)+"\t"+(BADoff)); in fillLimitedX() 453 assert(score>=MINoff_SCORE || score==BADoff) : "Score overflow - use MSA2 instead"; in fillLimitedX() 552 assert(maxScore>=BADoff); in fillLimitedX() 588 …assert(subfloor>BADoff && subfloor*2>BADoff) : (read.length-1)+", "+maxGain+", "+subfloor+", "+(su… in fillUnlimited() [all …]
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H A D | MultiStateAligner9Flat.java | 54 Arrays.fill(vertLimit, BADoff); in MultiStateAligner9Flat() 55 Arrays.fill(horizLimit, BADoff); in MultiStateAligner9Flat() 64 packed[matrix][i][j]|=BADoff; in MultiStateAligner9Flat() 146 Arrays.fill(packed[x][y], 1, columns+1, BADoff); in fillLimitedX() 154 Arrays.fill(packed[x][rows], 1, columns+1, BADoff); in fillLimitedX() 168 assert(subfloor>BADoff); //TODO: Actually, it needs to be substantially more. in fillLimitedX() 169 assert(subfloor<minScore_off) : minScore_off+", "+floor+", "+BADoff+", "+subfloor; in fillLimitedX() 177 System.out.println("BADoff="+(BADoff>>SCOREOFFSET)+"\t"+(BADoff)); in fillLimitedX() 561 assert(maxScore>=BADoff); in fillLimitedX() 608 …assert(subfloor>BADoff && subfloor*2>BADoff) : (read.length-1)+", "+maxGain+", "+subfloor+", "+(su… in fillUnlimited() [all …]
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H A D | MultiStateAligner9PacBio.java | 54 Arrays.fill(vertLimit, BADoff); in MultiStateAligner9PacBio() 55 Arrays.fill(horizLimit, BADoff); in MultiStateAligner9PacBio() 64 packed[matrix][i][j]|=BADoff; in MultiStateAligner9PacBio() 146 Arrays.fill(packed[x][y], 1, columns+1, BADoff); in fillLimitedX() 154 Arrays.fill(packed[x][rows], 1, columns+1, BADoff); in fillLimitedX() 168 assert(subfloor>BADoff); //TODO: Actually, it needs to be substantially more. in fillLimitedX() 169 assert(subfloor<minScore_off) : minScore_off+", "+floor+", "+BADoff+", "+subfloor; in fillLimitedX() 177 System.out.println("BADoff="+(BADoff>>SCOREOFFSET)+"\t"+(BADoff)); in fillLimitedX() 561 assert(maxScore>=BADoff); in fillLimitedX() 608 …assert(subfloor>BADoff && subfloor*2>BADoff) : (read.length-1)+", "+maxGain+", "+subfloor+", "+(su… in fillUnlimited() [all …]
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H A D | MultiStateAligner11tsJNI.java | 57 Arrays.fill(vertLimit, BADoff); in MultiStateAligner11tsJNI() 58 Arrays.fill(horizLimit, BADoff); in MultiStateAligner11tsJNI() 63 packed[(matrix)*(maxRows+1)*(maxColumns+1)+(i)*(maxColumns+1)+(j)]|=BADoff; in MultiStateAligner11tsJNI() 1516 public static final int BADoff=(BAD<<SCOREOFFSET);
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/dports/biology/bbmap/bbmap/jni/ |
H A D | MultiStateAligner11tsJNI.c | 96 #define BADoff (BAD<<SCOREOFFSET) macro 401 packed[x*sizeXY+tmp+i]=BADoff; in fillLimitedX()
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