/dports/biology/bbmap/bbmap/current/aligner/ |
H A D | MultiStateAligner9PacBioAdapter2.java | 657 scoreMS=scoreFromDiag+POINTSoff_NOCALL; in fillUnlimited() 700 int scoreMS=scoreFromDiag+POINTSoff_DEL; in fillUnlimited() 743 int scoreMS=scoreFromDiag+POINTSoff_INS; in fillUnlimited() 830 if(scoreFromDiag>=scoreFromDel && scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 857 if(scoreFromDiag>=scoreFromDel){prev=MODE_MS;} 870 if(scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 941 if(scoreFromDiag>=scoreFromDel && scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 959 if(scoreFromDiag>=scoreFromDel){prev=MODE_MS;} 970 if(scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 1064 if(scoreFromDiag>=scoreFromDel && scoreFromDiag>=scoreFromIns){prev=MODE_MS;} [all …]
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H A D | MultiStateAligner9PacBioAdapter.java | 584 scoreMS=scoreFromDiag+POINTSoff_NOCALL; in fillUnlimited() 624 final int scoreFromDiag=packed[MODE_MS][row][col-1]&SCOREMASK; in fillUnlimited() 627 int scoreMS=scoreFromDiag+POINTSoff_DEL; in fillUnlimited() 658 final int scoreFromDiag=packed[MODE_MS][row-1][col]&SCOREMASK; in fillUnlimited() 661 int scoreMS=scoreFromDiag+POINTSoff_INS; in fillUnlimited() 748 if(scoreFromDiag>=scoreFromDel && scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 775 if(scoreFromDiag>=scoreFromDel){prev=MODE_MS;} 788 if(scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 885 if(scoreFromDiag>=scoreFromDel && scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 896 if(scoreFromDiag>=scoreFromDel){prev=MODE_MS;} [all …]
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H A D | MultiStateAligner9PacBioAdapter3.java | 584 scoreMS=scoreFromDiag+POINTSoff_NOCALL; in fillUnlimited() 624 final int scoreFromDiag=packed[MODE_MS][row][col-1]&SCOREMASK; in fillUnlimited() 627 int scoreMS=scoreFromDiag+POINTSoff_DEL; in fillUnlimited() 665 final int scoreFromDiag=packed[MODE_MS][row-1][col]&SCOREMASK; in fillUnlimited() 668 int scoreMS=scoreFromDiag+POINTSoff_INS; in fillUnlimited() 754 if(scoreFromDiag>=scoreFromDel && scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 781 if(scoreFromDiag>=scoreFromDel){prev=MODE_MS;} 794 if(scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 891 if(scoreFromDiag>=scoreFromDel && scoreFromDiag>=scoreFromIns){prev=MODE_MS;} in score() 902 if(scoreFromDiag>=scoreFromDel){prev=MODE_MS;} in score() [all …]
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H A D | MultiStateAligner9PacBioAdapter_WithBarriers.java | 668 scoreMS=scoreFromDiag+POINTSoff_NOCALL; in fillUnlimited() 713 int scoreMS=scoreFromDiag+POINTSoff_DEL; in fillUnlimited() 765 int scoreMS=scoreFromDiag+POINTSoff_INS; in fillUnlimited() 933 int scoreMS=scoreFromDiag+POINTSoff_DEL; 971 int scoreMS=scoreFromDiag+POINTSoff_INS; 1074 if(scoreFromDiag>=scoreFromDel && scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 1101 if(scoreFromDiag>=scoreFromDel){prev=MODE_MS;} 1118 if(scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 1266 if(scoreFromDiag>=scoreFromDel && scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 1277 if(scoreFromDiag>=scoreFromDel){prev=MODE_MS;} [all …]
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H A D | SingleStateAlignerFlatFloat.java | 119 final float scoreFromDiag=packed[row-1][col-1]; in fillUnlimited() 134 diagScore=scoreFromDiag+(defined ? diagScore : POINTS_NOREF)*refWeights[rpos]; in fillUnlimited() 172 final float scoreFromDiag=packed[row-1][col-1]; 181 …final float diagScore=scoreFromDiag+(defined ? (match ? diagScoreM : diagScoreS) : POINTS_NOREF)*r… 200 final float scoreFromDiag=packed[row-1][col-1]; in getState() local 209 …final float diagScore=scoreFromDiag+(defined ? (match ? diagScoreM : diagScoreS) : POINTS_NOREF)*r… in getState()
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H A D | SingleStateAlignerFlat2_1D.java | 102 final int scoreFromDiag=get(row-1, col-1); in fillUnlimited() 113 diagScore=scoreFromDiag+(defined ? diagScore : POINTS_NOREF); in fillUnlimited() 150 final int scoreFromDiag=get(row-1, col-1); 160 final int diagScore=scoreFromDiag+(defined ? (match ? diagScoreM : diagScoreS) : POINTS_NOREF);
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H A D | SingleStateAlignerFlat2.java | 116 final int scoreFromDiag=packed[row-1][col-1]; in fillUnlimited() 127 diagScore=scoreFromDiag+(defined ? diagScore : POINTS_NOREF); in fillUnlimited() 164 final int scoreFromDiag=packed[row-1][col-1]; 174 final int diagScore=scoreFromDiag+(defined ? (match ? diagScoreM : diagScoreS) : POINTS_NOREF);
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H A D | SingleStateAlignerFlat3.java | 116 final int scoreFromDiag=packed[row-1][col-1]; in fillUnlimited() 127 diagScore=scoreFromDiag+(defined ? diagScore : POINTS_NOREF); in fillUnlimited() 164 final int scoreFromDiag=packed[row-1][col-1]; 174 final int diagScore=scoreFromDiag+(defined ? (match ? diagScoreM : diagScoreS) : POINTS_NOREF);
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H A D | SingleStateAlignerFlat2Amino.java | 115 final int scoreFromDiag=packed[row-1][col-1]; in fillUnlimited() 126 diagScore=scoreFromDiag+(defined ? diagScore : POINTS_NOREF); in fillUnlimited() 163 final int scoreFromDiag=packed[row-1][col-1]; 173 final int diagScore=scoreFromDiag+(defined ? (match ? diagScoreM : diagScoreS) : POINTS_NOREF);
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H A D | SingleStateAlignerPacBioAdapter.java | 113 final int scoreFromDiag=valueFromDiag&HIGHMASK; in fillUnlimited() 136 diagScore=scoreFromDiag+(rBase!='N' ? diagScore : POINTSoff_NOREF_MODE_SUB); in fillUnlimited()
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H A D | SingleStateAlignerFlat.java | 135 final int scoreFromDiag=valueFromDiag&HIGHMASK; in fillUnlimited() 158 diagScore=scoreFromDiag+(defined ? diagScore : POINTSoff_NOREF_MODE_SUB); in fillUnlimited()
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/dports/biology/bbmap/bbmap/current/align2/ |
H A D | MultiStateAligner11ts.java | 752 scoreMS=scoreFromDiag+POINTSoff_NOCALL; in fillUnlimited() 800 int scoreMS=scoreFromDiag+POINTSoff_DEL; in fillUnlimited() 860 int scoreMS=scoreFromDiag+POINTSoff_INS; in fillUnlimited() 1033 int scoreMS=scoreFromDiag+POINTSoff_DEL; in fillQ() 1071 int scoreMS=scoreFromDiag+POINTSoff_INS; in fillQ() 1175 if(scoreFromDiag>=scoreFromDel && scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 1202 if(scoreFromDiag>=scoreFromDel){prev=MODE_MS;} 1219 if(scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 1372 if(scoreFromDiag>=scoreFromDel && scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 1383 if(scoreFromDiag>=scoreFromDel){prev=MODE_MS;} [all …]
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H A D | MultiStateAligner9XFlat.java | 690 scoreMS=scoreFromDiag+POINTSoff_NOCALL; in fillUnlimited() 735 int scoreMS=scoreFromDiag+POINTSoff_DEL; in fillUnlimited() 784 int scoreMS=scoreFromDiag+POINTSoff_INS; in fillUnlimited() 951 int scoreMS=scoreFromDiag+POINTSoff_DEL; 986 int scoreMS=scoreFromDiag+POINTSoff_INS; 1088 if(scoreFromDiag>=scoreFromDel && scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 1115 if(scoreFromDiag>=scoreFromDel){prev=MODE_MS;} 1132 if(scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 1285 if(scoreFromDiag>=scoreFromDel && scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 1296 if(scoreFromDiag>=scoreFromDel){prev=MODE_MS;} [all …]
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H A D | MultiStateAligner9ts.java | 677 scoreMS=scoreFromDiag+POINTSoff_NOCALL; in fillUnlimited() 722 int scoreMS=scoreFromDiag+POINTSoff_DEL; in fillUnlimited() 774 int scoreMS=scoreFromDiag+POINTSoff_INS; in fillUnlimited() 943 int scoreMS=scoreFromDiag+POINTSoff_DEL; 981 int scoreMS=scoreFromDiag+POINTSoff_INS; 1084 if(scoreFromDiag>=scoreFromDel && scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 1111 if(scoreFromDiag>=scoreFromDel){prev=MODE_MS;} 1128 if(scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 1280 if(scoreFromDiag>=scoreFromDel && scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 1291 if(scoreFromDiag>=scoreFromDel){prev=MODE_MS;} [all …]
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H A D | MultiStateAligner9Flat.java | 697 scoreMS=scoreFromDiag+POINTSoff_NOCALL; in fillUnlimited() 742 int scoreMS=scoreFromDiag+POINTSoff_DEL; in fillUnlimited() 794 int scoreMS=scoreFromDiag+POINTSoff_INS; in fillUnlimited() 963 int scoreMS=scoreFromDiag+POINTSoff_DEL; 1001 int scoreMS=scoreFromDiag+POINTSoff_INS; 1104 if(scoreFromDiag>=scoreFromDel && scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 1131 if(scoreFromDiag>=scoreFromDel){prev=MODE_MS;} 1148 if(scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 1301 if(scoreFromDiag>=scoreFromDel && scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 1312 if(scoreFromDiag>=scoreFromDel){prev=MODE_MS;} [all …]
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H A D | MultiStateAligner9PacBio.java | 697 scoreMS=scoreFromDiag+POINTSoff_NOCALL; in fillUnlimited() 742 int scoreMS=scoreFromDiag+POINTSoff_DEL; in fillUnlimited() 794 int scoreMS=scoreFromDiag+POINTSoff_INS; in fillUnlimited() 963 int scoreMS=scoreFromDiag+POINTSoff_DEL; 1001 int scoreMS=scoreFromDiag+POINTSoff_INS; 1104 if(scoreFromDiag>=scoreFromDel && scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 1131 if(scoreFromDiag>=scoreFromDel){prev=MODE_MS;} 1148 if(scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 1301 if(scoreFromDiag>=scoreFromDel && scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 1312 if(scoreFromDiag>=scoreFromDel){prev=MODE_MS;} [all …]
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H A D | MultiStateAligner11tsJNI.java | 178 int scoreMS=scoreFromDiag+(prevMatch ? POINTSoff_MATCH2 : POINTSoff_MATCH); in fillQ() 204 int scoreMS=scoreFromDiag+(prevMatch ? (streak<=1 ? POINTSoff_SUBR : POINTSoff_SUB) : in fillQ() 238 …final int scoreFromDiag=packed[(MODE_MS)*(maxRows+1)*(maxColumns+1)+(row)*(maxColumns+1)+(col-1)]&… in fillQ() 241 int scoreMS=scoreFromDiag+POINTSoff_DEL; in fillQ() 274 int scoreMS=scoreFromDiag+POINTSoff_INS; in fillQ() 358 if(scoreFromDiag>=scoreFromDel && scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 384 if(scoreFromDiag>=scoreFromDel){prev=MODE_MS;} 401 if(scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 546 if(scoreFromDiag>=scoreFromDel && scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 557 if(scoreFromDiag>=scoreFromDel){prev=MODE_MS;} [all …]
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H A D | MultiStateAligner10ts.java | 1646 scoreMS=scoreFromDiag+POINTSoff_NOCALL; 1691 int scoreMS=scoreFromDiag+POINTSoff_DEL; 1743 int scoreMS=scoreFromDiag+POINTSoff_INS; 1912 int scoreMS=scoreFromDiag+POINTSoff_DEL; 1950 int scoreMS=scoreFromDiag+POINTSoff_INS; 2055 if(scoreFromDiag>=scoreFromDel && scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 2082 if(scoreFromDiag>=scoreFromDel){prev=MODE_MS;} 2099 if(scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 2249 if(scoreFromDiag>=scoreFromDel && scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 2260 if(scoreFromDiag>=scoreFromDel){prev=MODE_MS;} [all …]
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/dports/biology/bbmap/bbmap/jni/ |
H A D | MultiStateAligner11tsJNI.c | 154 const jint scoreFromDiag=packed[idxMS+tmp1+col-1]&SCOREMASK; in fillUnlimited() local 163 const jint scoreMS=scoreFromDiag+(prevMatch ? POINTSoff_MATCH2 : POINTSoff_MATCH); in fillUnlimited() 187 scoreMS=scoreFromDiag+(prevMatch ? (streak<=1 ? POINTSoff_SUBR : POINTSoff_SUB) : in fillUnlimited() 190 scoreMS=scoreFromDiag+POINTSoff_NOCALL; in fillUnlimited() 225 const jint scoreFromDiag=packed[idxMS+tmp2+col-1]&SCOREMASK; in fillUnlimited() local 228 jint scoreMS=scoreFromDiag+POINTSoff_DEL; in fillUnlimited() 267 const jint scoreFromDiag=packed[idxMS+tmp1+col]&SCOREMASK; in fillUnlimited() local 270 const jint scoreMS=scoreFromDiag+POINTSoff_INS; in fillUnlimited()
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