/dports/biology/bbmap/bbmap/current/aligner/ |
H A D | MultiStateAligner9PacBioAdapter2.java | 391 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() [all …]
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H A D | MultiStateAligner9PacBioAdapter.java | 334 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() [all …]
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H A D | MultiStateAligner9PacBioAdapter3.java | 319 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() [all …]
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H A D | MultiStateAligner9PacBioAdapter_WithBarriers.java | 379 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); [all …]
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H A D | SingleStateAlignerPacBioAdapter.java | 153 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;
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H A D | SingleStateAlignerFlat.java | 176 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;
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/dports/biology/bbmap/bbmap/current/align2/ |
H A D | MultiStateAligner11ts.java | 403 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() [all …]
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H A D | MultiStateAligner9XFlat.java | 396 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); [all …]
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H A D | MultiStateAligner9ts.java | 389 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); [all …]
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H A D | MultiStateAligner10ts.java | 406 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); [all …]
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H A D | MultiStateAligner9Flat.java | 398 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); [all …]
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H A D | MultiStateAligner9PacBio.java | 398 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); [all …]
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H A D | MultiStateAligner11tsJNI.java | 200 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; [all …]
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/dports/biology/bbmap/bbmap/jni/ |
H A D | MultiStateAligner11tsJNI.c | 39 #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() [all …]
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