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

/dports/biology/bbmap/bbmap/current/aligner/
H A DMultiStateAligner9PacBioAdapter2.java391 assert((score&SCOREMASK)==score); in fillLimitedX() argument
454 assert((score&SCOREMASK)==score); in fillLimitedX() argument
515 assert((score&SCOREMASK)==score); in fillLimitedX() argument
539 int x=packed[state][rows][col]&SCOREMASK; in fillLimitedX()
646 assert((score&SCOREMASK)==score); in fillUnlimited()
686 assert((score&SCOREMASK)==score); in fillUnlimited()
697 final int scoreFromDiag=packed[MODE_MS][row][col-1]&SCOREMASK; in fillUnlimited()
698 final int scoreFromDel=packed[MODE_DEL][row][col-1]&SCOREMASK; in fillUnlimited()
731 assert((score&SCOREMASK)==score); in fillUnlimited()
774 assert((score&SCOREMASK)==score); in fillUnlimited()
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H A DMultiStateAligner9PacBioAdapter.java334 assert((score&SCOREMASK)==score); in fillLimitedX() argument
387 assert((score&SCOREMASK)==score); in fillLimitedX() argument
446 assert((score&SCOREMASK)==score); in fillLimitedX() argument
470 int x=packed[state][rows][col]&SCOREMASK; in fillLimitedX()
574 assert((score&SCOREMASK)==score); in fillUnlimited()
613 assert((score&SCOREMASK)==score); in fillUnlimited()
624 final int scoreFromDiag=packed[MODE_MS][row][col-1]&SCOREMASK; in fillUnlimited()
625 final int scoreFromDel=packed[MODE_DEL][row][col-1]&SCOREMASK; in fillUnlimited()
649 assert((score&SCOREMASK)==score); in fillUnlimited()
690 assert((score&SCOREMASK)==score); in fillUnlimited()
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H A DMultiStateAligner9PacBioAdapter3.java319 assert((score&SCOREMASK)==score); in fillLimitedX() argument
380 assert((score&SCOREMASK)==score); in fillLimitedX() argument
439 assert((score&SCOREMASK)==score); in fillLimitedX() argument
463 int x=packed[state][rows][col]&SCOREMASK; in fillLimitedX()
574 assert((score&SCOREMASK)==score); in fillUnlimited()
613 assert((score&SCOREMASK)==score); in fillUnlimited()
624 final int scoreFromDiag=packed[MODE_MS][row][col-1]&SCOREMASK; in fillUnlimited()
625 final int scoreFromDel=packed[MODE_DEL][row][col-1]&SCOREMASK; in fillUnlimited()
656 assert((score&SCOREMASK)==score); in fillUnlimited()
697 assert((score&SCOREMASK)==score); in fillUnlimited()
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H A DMultiStateAligner9PacBioAdapter_WithBarriers.java379 assert((score&SCOREMASK)==score); in fillLimitedX() argument
447 assert((score&SCOREMASK)==score); in fillLimitedX() argument
509 assert((score&SCOREMASK)==score); in fillLimitedX() argument
657 assert((score&SCOREMASK)==score); in fillUnlimited()
697 assert((score&SCOREMASK)==score); in fillUnlimited() argument
749 assert((score&SCOREMASK)==score); in fillUnlimited()
796 assert((score&SCOREMASK)==score); in fillUnlimited()
885 assert((score&SCOREMASK)==score);
919 assert((score&SCOREMASK)==score);
959 assert((score&SCOREMASK)==score);
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H A DSingleStateAlignerPacBioAdapter.java153 if((x&SCOREMASK)>maxScore){ in fillUnlimited()
239 int score=packed[maxRow][maxCol]&SCOREMASK; //Or zero, if it is to be recalculated
390 public static final int SCOREMASK=(~((-1)<<SCOREBITS))<<SCOREOFFSET;
391 public static final int HIGHMASK=SCOREMASK|STARTMASK;
H A DSingleStateAlignerFlat.java176 if((x&SCOREMASK)>maxScore){ in fillUnlimited()
346 int score=packed[maxRow][maxCol]&SCOREMASK; //Or zero, if it is to be recalculated
503 public static final int SCOREMASK=(~((-1)<<SCOREBITS))<<SCOREOFFSET;
504 public static final int HIGHMASK=SCOREMASK|STARTMASK;
/dports/biology/bbmap/bbmap/current/align2/
H A DMultiStateAligner11ts.java403 assert((score&SCOREMASK)==score); in fillLimitedX() argument
471 assert((score&SCOREMASK)==score); in fillLimitedX() argument
533 assert((score&SCOREMASK)==score); in fillLimitedX() argument
734 assert((score&SCOREMASK)==score); in fillUnlimited()
779 assert((score&SCOREMASK)==score); in fillUnlimited()
840 assert((score&SCOREMASK)==score); in fillUnlimited()
886 assert((score&SCOREMASK)==score); in fillUnlimited()
983 assert((score&SCOREMASK)==score); in fillQ()
1019 assert((score&SCOREMASK)==score); in fillQ()
1059 assert((score&SCOREMASK)==score); in fillQ()
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H A DMultiStateAligner9XFlat.java396 assert((score&SCOREMASK)==score); in fillLimitedX() argument
461 assert((score&SCOREMASK)==score); in fillLimitedX() argument
522 assert((score&SCOREMASK)==score); in fillLimitedX() argument
680 assert((score&SCOREMASK)==score); in fillUnlimited()
719 assert((score&SCOREMASK)==score); in fillUnlimited() argument
768 assert((score&SCOREMASK)==score); in fillUnlimited()
814 assert((score&SCOREMASK)==score); in fillUnlimited()
904 assert((score&SCOREMASK)==score);
937 assert((score&SCOREMASK)==score);
974 assert((score&SCOREMASK)==score);
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H A DMultiStateAligner9ts.java389 assert((score&SCOREMASK)==score); in fillLimitedX() argument
457 assert((score&SCOREMASK)==score); in fillLimitedX() argument
519 assert((score&SCOREMASK)==score); in fillLimitedX() argument
666 assert((score&SCOREMASK)==score); in fillUnlimited()
706 assert((score&SCOREMASK)==score); in fillUnlimited() argument
758 assert((score&SCOREMASK)==score); in fillUnlimited()
805 assert((score&SCOREMASK)==score); in fillUnlimited()
895 assert((score&SCOREMASK)==score);
929 assert((score&SCOREMASK)==score);
969 assert((score&SCOREMASK)==score);
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H A DMultiStateAligner10ts.java406 assert((score&SCOREMASK)==score); in fillLimitedX() argument
474 assert((score&SCOREMASK)==score); in fillLimitedX() argument
536 assert((score&SCOREMASK)==score); in fillLimitedX() argument
881 assert((score&SCOREMASK)==score); in fillBanded1() argument
949 assert((score&SCOREMASK)==score); in fillBanded1() argument
1011 assert((score&SCOREMASK)==score); in fillBanded1() argument
1413 assert((score&SCOREMASK)==score);
1480 assert((score&SCOREMASK)==score);
1727 assert((score&SCOREMASK)==score);
1774 assert((score&SCOREMASK)==score);
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H A DMultiStateAligner9Flat.java398 assert((score&SCOREMASK)==score); in fillLimitedX() argument
466 assert((score&SCOREMASK)==score); in fillLimitedX() argument
528 assert((score&SCOREMASK)==score); in fillLimitedX() argument
686 assert((score&SCOREMASK)==score); in fillUnlimited()
726 assert((score&SCOREMASK)==score); in fillUnlimited() argument
778 assert((score&SCOREMASK)==score); in fillUnlimited()
825 assert((score&SCOREMASK)==score); in fillUnlimited()
915 assert((score&SCOREMASK)==score);
949 assert((score&SCOREMASK)==score);
989 assert((score&SCOREMASK)==score);
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H A DMultiStateAligner9PacBio.java398 assert((score&SCOREMASK)==score); in fillLimitedX() argument
466 assert((score&SCOREMASK)==score); in fillLimitedX() argument
528 assert((score&SCOREMASK)==score); in fillLimitedX() argument
686 assert((score&SCOREMASK)==score); in fillUnlimited()
726 assert((score&SCOREMASK)==score); in fillUnlimited() argument
778 assert((score&SCOREMASK)==score); in fillUnlimited()
825 assert((score&SCOREMASK)==score); in fillUnlimited()
915 assert((score&SCOREMASK)==score);
949 assert((score&SCOREMASK)==score);
989 assert((score&SCOREMASK)==score);
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H A DMultiStateAligner11tsJNI.java200 assert((score&SCOREMASK)==score); in fillQ()
230 assert((score&SCOREMASK)==score); in fillQ()
238 … scoreFromDiag=packed[(MODE_MS)*(maxRows+1)*(maxColumns+1)+(row)*(maxColumns+1)+(col-1)]&SCOREMASK; in fillQ()
239 … scoreFromDel=packed[(MODE_DEL)*(maxRows+1)*(maxColumns+1)+(row)*(maxColumns+1)+(col-1)]&SCOREMASK; in fillQ()
265 assert((score&SCOREMASK)==score); in fillQ()
271 … scoreFromDiag=packed[(MODE_MS)*(maxRows+1)*(maxColumns+1)+(row-1)*(maxColumns+1)+(col)]&SCOREMASK; in fillQ()
272 … scoreFromIns=packed[(MODE_INS)*(maxRows+1)*(maxColumns+1)+(row-1)*(maxColumns+1)+(col)]&SCOREMASK; in fillQ()
294 assert((score&SCOREMASK)==score); in fillQ()
306 int x=packed[(state)*(maxRows+1)*(maxColumns+1)+(rows)*(maxColumns+1)+(col)]&SCOREMASK; in fillQ()
382 … scoreFromDiag=packed[(MODE_MS)*(maxRows+1)*(maxColumns+1)+(row)*(maxColumns+1)+(col-1)]&SCOREMASK;
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/dports/biology/bbmap/bbmap/jni/
H A DMultiStateAligner11tsJNI.c39 #define SCOREMASK ((~((-1)<<SCOREBITS))<<SCOREOFFSET) macro
154 const jint scoreFromDiag=packed[idxMS+tmp1+col-1]&SCOREMASK; in fillUnlimited()
155 const jint scoreFromDel=packed[idxDEL+tmp1+col-1]&SCOREMASK; in fillUnlimited()
156 const jint scoreFromIns=packed[idxINS+tmp1+col-1]&SCOREMASK; in fillUnlimited()
225 const jint scoreFromDiag=packed[idxMS+tmp2+col-1]&SCOREMASK; in fillUnlimited()
226 const jint scoreFromDel=packed[idxDEL+tmp2+col-1]&SCOREMASK; in fillUnlimited()
267 const jint scoreFromDiag=packed[idxMS+tmp1+col]&SCOREMASK; in fillUnlimited()
268 const jint scoreFromIns=packed[idxINS+tmp1+col]&SCOREMASK; in fillUnlimited()
299 const int x=packed[(state)*sizeXY+tmp+col]&SCOREMASK; in fillUnlimited()
488 const jint scoreFromDiag_INS=packed[idxMS+tmp1+col]&SCOREMASK; in fillLimitedX()
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