Home
last modified time | relevance | path

Searched refs:SCOREOFFSET (Results 1 – 15 of 15) sorted by relevance

/dports/biology/bbmap/bbmap/current/aligner/
H A DSingleStateAlignerPacBioAdapter.java160 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 …]
H A DMultiStateAligner9PacBioAdapter2.java185 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 …]
H A DMultiStateAligner9PacBioAdapter3.java125 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 …]
H A DMultiStateAligner9PacBioAdapter.java129 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 …]
H A DMultiStateAligner9PacBioAdapter_WithBarriers.java170 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 …]
H A DSingleStateAlignerFlat.java183 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);
/dports/biology/bbmap/bbmap/jni/
H A DMultiStateAligner11tsJNI.c36 #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 …]
/dports/biology/bbmap/bbmap/current/align2/
H A DMultiStateAligner10ts.java392 …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 …]
H A DMultiStateAligner11ts.java166 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 …]
H A DMultiStateAligner9ts.java154 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 …]
H A DMultiStateAligner9Flat.java163 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 …]
H A DMultiStateAligner9PacBio.java163 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 …]
H A DMultiStateAligner9XFlat.java162 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 …]
H A DMultiStateAligner11tsJNI.java194 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 …]
H A DMSA.java570 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