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Searched refs:BADoff (Results 1 – 14 of 14) sorted by relevance

/dports/biology/bbmap/bbmap/current/aligner/
H A DMultiStateAligner9PacBioAdapter.java45 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()
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H A DMultiStateAligner9PacBioAdapter2.java107 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()
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H A DMultiStateAligner9PacBioAdapter3.java56 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()
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H A DSingleStateAlignerPacBioAdapter.java37 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);
H A DMultiStateAligner9PacBioAdapter_WithBarriers.java76 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()
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H A DSingleStateAlignerFlat.java528 public static final int BADoff=(BAD<<SCOREOFFSET);
/dports/biology/bbmap/bbmap/current/align2/
H A DMultiStateAligner10ts.java59 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);
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H A DMultiStateAligner11ts.java58 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()
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H A DMultiStateAligner9XFlat.java54 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()
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H A DMultiStateAligner9ts.java57 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()
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H A DMultiStateAligner9Flat.java54 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()
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H A DMultiStateAligner9PacBio.java54 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()
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H A DMultiStateAligner11tsJNI.java57 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);
/dports/biology/bbmap/bbmap/jni/
H A DMultiStateAligner11tsJNI.c96 #define BADoff (BAD<<SCOREOFFSET) macro
401 packed[x*sizeXY+tmp+i]=BADoff; in fillLimitedX()