/dports/biology/bbmap/bbmap/current/aligner/ |
H A D | SingleStateAlignerPacBioAdapter.java | 160 maxScore>>=SCOREOFFSET; in fillUnlimited() 284 score>>=SCOREOFFSET; 386 public static final int SCOREOFFSET=LOWBITS; 430 public static final int POINTSoff_SUB=(POINTS_SUB<<SCOREOFFSET); 431 public static final int POINTSoff_SUB2=(POINTS_SUB2<<SCOREOFFSET); 432 public static final int POINTSoff_INS=(POINTS_INS<<SCOREOFFSET); 433 public static final int POINTSoff_INS2=(POINTS_INS2<<SCOREOFFSET); 434 public static final int POINTSoff_DEL=(POINTS_DEL<<SCOREOFFSET); 436 public static final int BADoff=(BAD<<SCOREOFFSET); 437 public static final int MAXoff_SCORE=MAX_SCORE<<SCOREOFFSET; [all …]
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H A D | MultiStateAligner9PacBioAdapter2.java | 185 final int minScore_off=(minScore<<SCOREOFFSET); in fillLimitedX() 377 …verbose2){System.err.println("MS: \tlimit2="+(limit2>>SCOREOFFSET)+"\t, score="+(score>>SCOREOFFSE… in fillLimitedX() 440 …erbose2){System.err.println("DEL: \tlimit2="+(limit2>>SCOREOFFSET)+"\t, score="+(score>>SCOREOFFSE… in fillLimitedX() 502 …erbose2){System.err.println("INS: \tlimit2="+(limit2>>SCOREOFFSET)+"\t, score="+(score>>SCOREOFFSE… in fillLimitedX() 559 maxScore>>=SCOREOFFSET; in fillLimitedX() field in MultiStateAligner9PacBioAdapter2 796 maxScore>>=SCOREOFFSET; in fillUnlimited() 1109 score>>=SCOREOFFSET; 1524 int num=num_>>SCOREOFFSET; 1678 public static final int SCOREOFFSET=TIMEBITS; 1756 public static final int BADoff=(BAD<<SCOREOFFSET); [all …]
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H A D | MultiStateAligner9PacBioAdapter3.java | 125 final int minScore_off=(minScore<<SCOREOFFSET); in fillLimitedX() 305 …verbose2){System.err.println("MS: \tlimit2="+(limit2>>SCOREOFFSET)+"\t, score="+(score>>SCOREOFFSE… in fillLimitedX() 366 …erbose2){System.err.println("DEL: \tlimit2="+(limit2>>SCOREOFFSET)+"\t, score="+(score>>SCOREOFFSE… in fillLimitedX() 426 …erbose2){System.err.println("INS: \tlimit2="+(limit2>>SCOREOFFSET)+"\t, score="+(score>>SCOREOFFSE… in fillLimitedX() 483 maxScore>>=SCOREOFFSET; in fillLimitedX() field in MultiStateAligner9PacBioAdapter3 719 maxScore>>=SCOREOFFSET; in fillUnlimited() 936 score>>=SCOREOFFSET; in score() local 1347 int num=num_>>SCOREOFFSET; 1510 public static final int SCOREOFFSET=TIMEBITS; 1568 public static final int BADoff=(BAD<<SCOREOFFSET); [all …]
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H A D | MultiStateAligner9PacBioAdapter.java | 129 final int minScore_off=(minScore<<SCOREOFFSET); in fillLimitedX() 320 …verbose2){System.err.println("MS: \tlimit2="+(limit2>>SCOREOFFSET)+"\t, score="+(score>>SCOREOFFSE… in fillLimitedX() 373 …erbose2){System.err.println("DEL: \tlimit2="+(limit2>>SCOREOFFSET)+"\t, score="+(score>>SCOREOFFSE… in fillLimitedX() 433 …erbose2){System.err.println("INS: \tlimit2="+(limit2>>SCOREOFFSET)+"\t, score="+(score>>SCOREOFFSE… in fillLimitedX() 490 maxScore>>=SCOREOFFSET; in fillLimitedX() field in MultiStateAligner9PacBioAdapter 712 maxScore>>=SCOREOFFSET; in fillUnlimited() 930 score>>=SCOREOFFSET; 1341 int num=num_>>SCOREOFFSET; 1465 public static final int SCOREOFFSET=TIMEBITS; 1514 public static final int BADoff=(BAD<<SCOREOFFSET); [all …]
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H A D | MultiStateAligner9PacBioAdapter_WithBarriers.java | 170 final int minScore_off=(minScore<<SCOREOFFSET); in fillLimitedX() 365 …verbose2){System.err.println("MS: \tlimit2="+(limit2>>SCOREOFFSET)+"\t, score="+(score>>SCOREOFFSE… in fillLimitedX() 433 …erbose2){System.err.println("DEL: \tlimit2="+(limit2>>SCOREOFFSET)+"\t, score="+(score>>SCOREOFFSE… in fillLimitedX() 496 …erbose2){System.err.println("INS: \tlimit2="+(limit2>>SCOREOFFSET)+"\t, score="+(score>>SCOREOFFSE… in fillLimitedX() 553 maxScore>>=SCOREOFFSET; in fillLimitedX() field in MultiStateAligner9PacBioAdapter_WithBarriers 818 maxScore>>=SCOREOFFSET; in fillUnlimited() 1022 maxScore>>=SCOREOFFSET; 1311 score>>=SCOREOFFSET; 2326 int num=num_>>SCOREOFFSET; 2487 public static final int SCOREOFFSET=TIMEBITS; [all …]
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H A D | SingleStateAlignerFlat.java | 183 maxScore>>=SCOREOFFSET; in fillUnlimited() 397 score>>=SCOREOFFSET; 499 public static final int SCOREOFFSET=LOWBITS; 503 public static final int SCOREMASK=(~((-1)<<SCOREBITS))<<SCOREOFFSET; 522 public static final int POINTSoff_NOREF=(POINTS_NOREF<<SCOREOFFSET); 524 public static final int POINTSoff_MATCH=(POINTS_MATCH<<SCOREOFFSET); 525 public static final int POINTSoff_SUB=(POINTS_SUB<<SCOREOFFSET); 526 public static final int POINTSoff_INS=(POINTS_INS<<SCOREOFFSET); 527 public static final int POINTSoff_DEL=(POINTS_DEL<<SCOREOFFSET); 528 public static final int BADoff=(BAD<<SCOREOFFSET);
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/dports/biology/bbmap/bbmap/jni/ |
H A D | MultiStateAligner11tsJNI.c | 36 #define SCOREOFFSET TIMEBITS macro 80 #define POINTSoff_SUB (POINTS_SUB<<SCOREOFFSET) 81 #define POINTSoff_SUBR (POINTS_SUBR<<SCOREOFFSET) 85 #define POINTSoff_INS (POINTS_INS<<SCOREOFFSET) 89 #define POINTSoff_DEL (POINTS_DEL<<SCOREOFFSET) 94 #define POINTSoff_GAP (POINTS_GAP<<SCOREOFFSET) 96 #define BADoff (BAD<<SCOREOFFSET) 97 #define MAXoff_SCORE (MAX_SCORE<<SCOREOFFSET) 98 #define MINoff_SCORE (MIN_SCORE<<SCOREOFFSET) 307 maxScore>>=SCOREOFFSET; in fillUnlimited() [all …]
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/dports/biology/bbmap/bbmap/current/align2/ |
H A D | MultiStateAligner10ts.java | 392 …verbose2){System.err.println("MS: \tlimit2="+(limit2>>SCOREOFFSET)+"\t, score="+(score>>SCOREOFFSE… in fillLimitedX() 460 …erbose2){System.err.println("DEL: \tlimit2="+(limit2>>SCOREOFFSET)+"\t, score="+(score>>SCOREOFFSE… in fillLimitedX() 523 …erbose2){System.err.println("INS: \tlimit2="+(limit2>>SCOREOFFSET)+"\t, score="+(score>>SCOREOFFSE… in fillLimitedX() 581 …erbose){System.err.println("maxscore="+(maxScore>>SCOREOFFSET)+", minscore="+(minScore_off>>SCOREO… in fillLimitedX() 587 maxScore>>=SCOREOFFSET; in fillLimitedX() field in MultiStateAligner10ts 1055 maxScore>>=SCOREOFFSET; in fillBanded1() 1529 maxScore>>=SCOREOFFSET; 1796 maxScore>>=SCOREOFFSET; 2001 maxScore>>=SCOREOFFSET; 2294 score>>=SCOREOFFSET; [all …]
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H A D | MultiStateAligner11ts.java | 166 final int minScore_off=(minScore<<SCOREOFFSET); in fillLimitedX() 389 …verbose2){System.err.println("MS: \tlimit2="+(limit2>>SCOREOFFSET)+"\t, score="+(score>>SCOREOFFSE… in fillLimitedX() 457 …erbose2){System.err.println("DEL: \tlimit2="+(limit2>>SCOREOFFSET)+"\t, score="+(score>>SCOREOFFSE… in fillLimitedX() 520 …erbose2){System.err.println("INS: \tlimit2="+(limit2>>SCOREOFFSET)+"\t, score="+(score>>SCOREOFFSE… in fillLimitedX() 578 …erbose){System.err.println("maxscore="+(maxScore>>SCOREOFFSET)+", minscore="+(minScore_off>>SCOREO… in fillLimitedX() 584 maxScore>>=SCOREOFFSET; in fillLimitedX() field in MultiStateAligner11ts 915 maxScore>>=SCOREOFFSET; in fillUnlimited() local 1123 maxScore>>=SCOREOFFSET; in fillQ() 1419 score>>=SCOREOFFSET; 2437 public static final int SCOREOFFSET=TIMEBITS; [all …]
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H A D | MultiStateAligner9ts.java | 154 final int minScore_off=(minScore<<SCOREOFFSET); in fillLimitedX() 375 …verbose2){System.err.println("MS: \tlimit2="+(limit2>>SCOREOFFSET)+"\t, score="+(score>>SCOREOFFSE… in fillLimitedX() 443 …erbose2){System.err.println("DEL: \tlimit2="+(limit2>>SCOREOFFSET)+"\t, score="+(score>>SCOREOFFSE… in fillLimitedX() 506 …erbose2){System.err.println("INS: \tlimit2="+(limit2>>SCOREOFFSET)+"\t, score="+(score>>SCOREOFFSE… in fillLimitedX() 563 maxScore>>=SCOREOFFSET; in fillLimitedX() field in MultiStateAligner9ts 827 maxScore>>=SCOREOFFSET; in fillUnlimited() 1032 maxScore>>=SCOREOFFSET; 1325 score>>=SCOREOFFSET; 2302 public static final int SCOREOFFSET=TIMEBITS; 2366 public static final int BADoff=(BAD<<SCOREOFFSET); [all …]
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H A D | MultiStateAligner9Flat.java | 163 final int minScore_off=(minScore<<SCOREOFFSET); in fillLimitedX() 384 …verbose2){System.err.println("MS: \tlimit2="+(limit2>>SCOREOFFSET)+"\t, score="+(score>>SCOREOFFSE… in fillLimitedX() 452 …erbose2){System.err.println("DEL: \tlimit2="+(limit2>>SCOREOFFSET)+"\t, score="+(score>>SCOREOFFSE… in fillLimitedX() 515 …erbose2){System.err.println("INS: \tlimit2="+(limit2>>SCOREOFFSET)+"\t, score="+(score>>SCOREOFFSE… in fillLimitedX() 573 …erbose){System.err.println("maxscore="+(maxScore>>SCOREOFFSET)+", minscore="+(minScore_off>>SCOREO… in fillLimitedX() 579 maxScore>>=SCOREOFFSET; in fillLimitedX() field in MultiStateAligner9Flat 847 maxScore>>=SCOREOFFSET; in fillUnlimited() 1052 maxScore>>=SCOREOFFSET; 1348 score>>=SCOREOFFSET; 2347 public static final int SCOREOFFSET=TIMEBITS; [all …]
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H A D | MultiStateAligner9PacBio.java | 163 final int minScore_off=(minScore<<SCOREOFFSET); in fillLimitedX() 384 …verbose2){System.err.println("MS: \tlimit2="+(limit2>>SCOREOFFSET)+"\t, score="+(score>>SCOREOFFSE… in fillLimitedX() 452 …erbose2){System.err.println("DEL: \tlimit2="+(limit2>>SCOREOFFSET)+"\t, score="+(score>>SCOREOFFSE… in fillLimitedX() 515 …erbose2){System.err.println("INS: \tlimit2="+(limit2>>SCOREOFFSET)+"\t, score="+(score>>SCOREOFFSE… in fillLimitedX() 573 …erbose){System.err.println("maxscore="+(maxScore>>SCOREOFFSET)+", minscore="+(minScore_off>>SCOREO… in fillLimitedX() 579 maxScore>>=SCOREOFFSET; in fillLimitedX() field in MultiStateAligner9PacBio 847 maxScore>>=SCOREOFFSET; in fillUnlimited() 1052 maxScore>>=SCOREOFFSET; 1348 score>>=SCOREOFFSET; 2347 public static final int SCOREOFFSET=TIMEBITS; [all …]
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H A D | MultiStateAligner9XFlat.java | 162 final int minScore_off=(minScore<<SCOREOFFSET); in fillLimitedX() 382 …verbose2){System.err.println("MS: \tlimit2="+(limit2>>SCOREOFFSET)+"\t, score="+(score>>SCOREOFFSE… in fillLimitedX() 447 …erbose2){System.err.println("DEL: \tlimit2="+(limit2>>SCOREOFFSET)+"\t, score="+(score>>SCOREOFFSE… in fillLimitedX() 509 …erbose2){System.err.println("INS: \tlimit2="+(limit2>>SCOREOFFSET)+"\t, score="+(score>>SCOREOFFSE… in fillLimitedX() 567 …erbose){System.err.println("maxscore="+(maxScore>>SCOREOFFSET)+", minscore="+(minScore_off>>SCOREO… in fillLimitedX() 573 maxScore>>=SCOREOFFSET; in fillLimitedX() field in MultiStateAligner9XFlat 836 maxScore>>=SCOREOFFSET; in fillUnlimited() 1036 maxScore>>=SCOREOFFSET; 1332 score>>=SCOREOFFSET; 2238 public static final int SCOREOFFSET=TIMEBITS; [all …]
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H A D | MultiStateAligner11tsJNI.java | 194 score+=(((int)baseScores[row-1])<<SCOREOFFSET); //modifier in fillQ() 314 maxScore>>=SCOREOFFSET; in fillQ() 591 score>>=SCOREOFFSET; 1455 public static final int SCOREOFFSET=TIMEBITS; 1500 public static final int POINTSoff_SUB=(POINTS_SUB<<SCOREOFFSET); 1505 public static final int POINTSoff_INS=(POINTS_INS<<SCOREOFFSET); 1509 public static final int POINTSoff_DEL=(POINTS_DEL<<SCOREOFFSET); 1516 public static final int BADoff=(BAD<<SCOREOFFSET); 1517 public static final int MAXoff_SCORE=MAX_SCORE<<SCOREOFFSET; 1518 public static final int MINoff_SCORE=MIN_SCORE<<SCOREOFFSET; [all …]
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H A D | MSA.java | 570 static void printMatrix(int[][][] packed, int readlen, int reflen, int TIMEMASK, int SCOREOFFSET){ in printMatrix() argument 572 printMatrix(packed, readlen, reflen, TIMEMASK, SCOREOFFSET, mode); in printMatrix() 576 …static void printMatrix(int[][][] packed, int readlen, int reflen, int TIMEMASK, int SCOREOFFSET, … in printMatrix() argument 580 System.out.println(toScorePacked(packed[mode][row], SCOREOFFSET, xlim)); in printMatrix() 606 public static final String toScorePacked(int[] a, int SCOREOFFSET, int lim){ in toScorePacked() argument 622 int num=a[j]>>SCOREOFFSET; in toScorePacked() 731 public abstract int SCOREOFFSET(); in SCOREOFFSET() method in MSA
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