/dports/biology/bbmap/bbmap/current/aligner/ |
H A D | MultiStateAligner9PacBioAdapter2.java | 621 int scoreD=scoreFromDel+POINTSoff_MATCH; in fillUnlimited() 698 final int scoreFromDel=packed[MODE_DEL][row][col-1]&SCOREMASK; in fillUnlimited() 701 int scoreD=scoreFromDel+(streak==0 ? POINTSoff_DEL : in fillUnlimited() 831 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} 856 final int scoreFromDel=packed[MODE_DEL][row][col-1]&SCOREMASK; local 857 if(scoreFromDiag>=scoreFromDel){prev=MODE_MS;} 942 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} 958 final int scoreFromDel=packed[MODE_DEL][row][col-1]&SCOREMASK; 959 if(scoreFromDiag>=scoreFromDel){prev=MODE_MS;} 1065 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} [all …]
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H A D | MultiStateAligner9PacBioAdapter.java | 540 final int scoreFromDel=packed[MODE_DEL][row-1][col-1]&SCOREMASK; in fillUnlimited() 549 int scoreD=scoreFromDel+POINTSoff_MATCH; in fillUnlimited() 625 final int scoreFromDel=packed[MODE_DEL][row][col-1]&SCOREMASK; in fillUnlimited() 628 int scoreD=scoreFromDel+delScoreArray[streak]; in fillUnlimited() 746 final int scoreFromDel=packed[MODE_DEL][row-1][col-1]&SCOREMASK; local 749 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} 774 final int scoreFromDel=packed[MODE_DEL][row][col-1]&SCOREMASK; 775 if(scoreFromDiag>=scoreFromDel){prev=MODE_MS;} 886 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} 895 final int scoreFromDel=packed[MODE_DEL][row][col-1]&SCOREMASK; [all …]
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H A D | SingleStateAlignerFlatFloat.java | 120 final float scoreFromDel=packed[row][col-1]; in fillUnlimited() 125 final float delScore=scoreFromDel+POINTS_DEL;//*delWeights[rpos]; in fillUnlimited() 173 final float scoreFromDel=packed[row][col-1]; 178 final float delScore=scoreFromDel+POINTS_DEL*delWeight; 201 final float scoreFromDel=packed[row][col-1]; in getState() local 206 final float delScore=scoreFromDel+POINTS_DEL; in getState()
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H A D | MultiStateAligner9PacBioAdapter3.java | 540 final int scoreFromDel=packed[MODE_DEL][row-1][col-1]&SCOREMASK; in fillUnlimited() 549 int scoreD=scoreFromDel+POINTSoff_MATCH; in fillUnlimited() 625 final int scoreFromDel=packed[MODE_DEL][row][col-1]&SCOREMASK; in fillUnlimited() 628 int scoreD=scoreFromDel+delScoreArray[streak]; in fillUnlimited() 752 final int scoreFromDel=packed[MODE_DEL][row-1][col-1]&SCOREMASK; local 755 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} 780 final int scoreFromDel=packed[MODE_DEL][row][col-1]&SCOREMASK; local 781 if(scoreFromDiag>=scoreFromDel){prev=MODE_MS;} 892 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} in score() 901 final int scoreFromDel=packed[MODE_DEL][row][col-1]&SCOREMASK; in score() local [all …]
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H A D | MultiStateAligner9PacBioAdapter_WithBarriers.java | 632 int scoreD=scoreFromDel+POINTSoff_MATCH; in fillUnlimited() 711 final int scoreFromDel=packed[MODE_DEL][row][col-1]&SCOREMASK; in fillUnlimited() 714 int scoreD=scoreFromDel+(streak==0 ? POINTSoff_DEL : in fillUnlimited() 859 int scoreD=scoreFromDel+POINTSoff_MATCH; 931 final int scoreFromDel=packed[MODE_DEL][row][col-1]&SCOREMASK; 934 int scoreD=scoreFromDel+(streak==0 ? POINTSoff_DEL : 1075 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} 1100 final int scoreFromDel=packed[MODE_DEL][row][col-1]&SCOREMASK; 1101 if(scoreFromDiag>=scoreFromDel){prev=MODE_MS;} 1267 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} [all …]
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H A D | SingleStateAlignerFlat2_1D.java | 103 final int scoreFromDel=get(row, col-1); in fillUnlimited() argument 108 final int delScore=scoreFromDel+POINTS_DEL; in fillUnlimited() 151 final int scoreFromDel=get(row, col-1); 157 final int delScore=scoreFromDel+POINTS_DEL;
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H A D | SingleStateAlignerFlat2.java | 117 final int scoreFromDel=packed[row][col-1]; in fillUnlimited() 122 final int delScore=scoreFromDel+POINTS_DEL; in fillUnlimited() 165 final int scoreFromDel=packed[row][col-1]; 171 final int delScore=scoreFromDel+POINTS_DEL;
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H A D | SingleStateAlignerFlat3.java | 117 final int scoreFromDel=packed[row][col-1]; in fillUnlimited() 122 final int delScore=scoreFromDel+POINTS_DEL; in fillUnlimited() 165 final int scoreFromDel=packed[row][col-1]; 171 final int delScore=scoreFromDel+POINTS_DEL;
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H A D | SingleStateAlignerFlat2Amino.java | 116 final int scoreFromDel=packed[row][col-1]; in fillUnlimited() 121 final int delScore=scoreFromDel+POINTS_DEL; in fillUnlimited() 164 final int scoreFromDel=packed[row][col-1]; 170 final int delScore=scoreFromDel+POINTS_DEL;
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H A D | SingleStateAlignerPacBioAdapter.java | 115 final int scoreFromDel=valueFromDel&HIGHMASK; in fillUnlimited() 132 final int delScore=scoreFromDel+delScoreArray[stateFromDel]; in fillUnlimited()
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H A D | SingleStateAlignerFlat.java | 137 final int scoreFromDel=valueFromDel&HIGHMASK; in fillUnlimited() 154 final int delScore=scoreFromDel+POINTSoff_DEL|MODE_DEL; in fillUnlimited()
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/dports/biology/bbmap/bbmap/current/align2/ |
H A D | MultiStateAligner11ts.java | 702 int scoreD=scoreFromDel+POINTSoff_MATCH; in fillUnlimited() 798 final int scoreFromDel=packed[MODE_DEL][row][col-1]&SCOREMASK; in fillUnlimited() local 805 int scoreD=scoreFromDel+(streak==0 ? POINTSoff_DEL : in fillUnlimited() 957 int scoreD=scoreFromDel+POINTSoff_MATCH; in fillQ() 1031 final int scoreFromDel=packed[MODE_DEL][row][col-1]&SCOREMASK; in fillQ() 1034 int scoreD=scoreFromDel+(streak==0 ? POINTSoff_DEL : in fillQ() 1176 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} 1201 final int scoreFromDel=packed[MODE_DEL][row][col-1]&SCOREMASK; 1202 if(scoreFromDiag>=scoreFromDel){prev=MODE_MS;} 1373 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} [all …]
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H A D | MultiStateAligner9XFlat.java | 655 int scoreD=scoreFromDel+POINTSoff_MATCH; in fillUnlimited() 733 final int scoreFromDel=packed[MODE_DEL][row][col-1]&SCOREMASK; in fillUnlimited() 736 int scoreD=scoreFromDel+(streak==0 ? POINTSoff_DEL : in fillUnlimited() 878 int scoreD=scoreFromDel+POINTSoff_MATCH; 949 final int scoreFromDel=packed[MODE_DEL][row][col-1]&SCOREMASK; 952 int scoreD=scoreFromDel+(streak==0 ? POINTSoff_DEL : 1089 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} 1114 final int scoreFromDel=packed[MODE_DEL][row][col-1]&SCOREMASK; 1115 if(scoreFromDiag>=scoreFromDel){prev=MODE_MS;} 1286 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} [all …]
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H A D | MultiStateAligner9ts.java | 641 int scoreD=scoreFromDel+POINTSoff_MATCH; in fillUnlimited() 720 final int scoreFromDel=packed[MODE_DEL][row][col-1]&SCOREMASK; in fillUnlimited() 723 int scoreD=scoreFromDel+(streak==0 ? POINTSoff_DEL : in fillUnlimited() 869 int scoreD=scoreFromDel+POINTSoff_MATCH; 941 final int scoreFromDel=packed[MODE_DEL][row][col-1]&SCOREMASK; 944 int scoreD=scoreFromDel+(streak==0 ? POINTSoff_DEL : 1085 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} 1110 final int scoreFromDel=packed[MODE_DEL][row][col-1]&SCOREMASK; 1111 if(scoreFromDiag>=scoreFromDel){prev=MODE_MS;} 1281 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} [all …]
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H A D | MultiStateAligner11tsJNI.java | 179 int scoreD=scoreFromDel+POINTSoff_MATCH; in fillQ() 206 …int scoreD=scoreFromDel+POINTSoff_SUB; //+2 to move it as close as possible to the deletion / inse… in fillQ() 239 …final int scoreFromDel=packed[(MODE_DEL)*(maxRows+1)*(maxColumns+1)+(row)*(maxColumns+1)+(col-1)]&… in fillQ() 242 int scoreD=scoreFromDel+(streak==0 ? POINTSoff_DEL : in fillQ() 358 if(scoreFromDiag>=scoreFromDel && scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 359 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} 383 …final int scoreFromDel=packed[(MODE_DEL)*(maxRows+1)*(maxColumns+1)+(row)*(maxColumns+1)+(col-1)]&… 384 if(scoreFromDiag>=scoreFromDel){prev=MODE_MS;} 546 if(scoreFromDiag>=scoreFromDel && scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 547 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} [all …]
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H A D | MultiStateAligner9Flat.java | 661 int scoreD=scoreFromDel+POINTSoff_MATCH; in fillUnlimited() 740 final int scoreFromDel=packed[MODE_DEL][row][col-1]&SCOREMASK; in fillUnlimited() 743 int scoreD=scoreFromDel+(streak==0 ? POINTSoff_DEL : in fillUnlimited() 889 int scoreD=scoreFromDel+POINTSoff_MATCH; 961 final int scoreFromDel=packed[MODE_DEL][row][col-1]&SCOREMASK; 964 int scoreD=scoreFromDel+(streak==0 ? POINTSoff_DEL : 1105 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} 1130 final int scoreFromDel=packed[MODE_DEL][row][col-1]&SCOREMASK; 1131 if(scoreFromDiag>=scoreFromDel){prev=MODE_MS;} 1302 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} [all …]
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H A D | MultiStateAligner9PacBio.java | 661 int scoreD=scoreFromDel+POINTSoff_MATCH; in fillUnlimited() 740 final int scoreFromDel=packed[MODE_DEL][row][col-1]&SCOREMASK; in fillUnlimited() 743 int scoreD=scoreFromDel+(streak==0 ? POINTSoff_DEL : in fillUnlimited() 889 int scoreD=scoreFromDel+POINTSoff_MATCH; 961 final int scoreFromDel=packed[MODE_DEL][row][col-1]&SCOREMASK; 964 int scoreD=scoreFromDel+(streak==0 ? POINTSoff_DEL : 1105 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} 1130 final int scoreFromDel=packed[MODE_DEL][row][col-1]&SCOREMASK; 1131 if(scoreFromDiag>=scoreFromDel){prev=MODE_MS;} 1302 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} [all …]
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H A D | MultiStateAligner10ts.java | 1610 int scoreD=scoreFromDel+POINTSoff_MATCH; 1689 final int scoreFromDel=packed[MODE_DEL][row][col-1]&SCOREMASK; 1692 int scoreD=scoreFromDel+(streak==0 ? POINTSoff_DEL : 1838 int scoreD=scoreFromDel+POINTSoff_MATCH; 1910 final int scoreFromDel=packed[MODE_DEL][row][col-1]&SCOREMASK; 1913 int scoreD=scoreFromDel+(streak==0 ? POINTSoff_DEL : 2056 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} 2081 final int scoreFromDel=packed[MODE_DEL][row][col-1]&SCOREMASK; 2082 if(scoreFromDiag>=scoreFromDel){prev=MODE_MS;} 2250 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} [all …]
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/dports/biology/bbmap/bbmap/jni/ |
H A D | MultiStateAligner11tsJNI.c | 155 const jint scoreFromDel=packed[idxDEL+tmp1+col-1]&SCOREMASK; in fillUnlimited() local 164 const jint scoreD=scoreFromDel+POINTSoff_MATCH; in fillUnlimited() 193 …const jint scoreD=scoreFromDel+POINTSoff_SUB; //+2 to move it as close as possible to the deletion… in fillUnlimited() 226 const jint scoreFromDel=packed[idxDEL+tmp2+col-1]&SCOREMASK; in fillUnlimited() local 229 jint scoreD=scoreFromDel+(streak==0 ? POINTSoff_DEL : in fillUnlimited()
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