/dports/biology/bbmap/bbmap/current/aligner/ |
H A D | MultiStateAligner9PacBioAdapter2.java | 622 int scoreI=scoreFromIns+POINTSoff_MATCH; in fillUnlimited() 661 int scoreI=scoreFromIns+POINTSoff_SUB; in fillUnlimited() 741 final int scoreFromIns=packed[MODE_INS][row-1][col]&SCOREMASK; in fillUnlimited() 745 int scoreI=scoreFromIns+(streak==0 ? POINTSoff_INS : in fillUnlimited() 831 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} 869 final int scoreFromIns=packed[MODE_INS][row-1][col]&SCOREMASK; 870 if(scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 942 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} 970 if(scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 1065 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} [all …]
|
H A D | MultiStateAligner9PacBioAdapter.java | 541 final int scoreFromIns=packed[MODE_INS][row-1][col-1]&SCOREMASK; in fillUnlimited() 550 int scoreI=scoreFromIns+POINTSoff_MATCH; in fillUnlimited() 588 int scoreI=scoreFromIns+POINTSoff_SUB; in fillUnlimited() 659 final int scoreFromIns=packed[MODE_INS][row-1][col]&SCOREMASK; in fillUnlimited() 663 int scoreI=scoreFromIns+insScoreArray[streak]; in fillUnlimited() 749 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} 787 final int scoreFromIns=packed[MODE_INS][row-1][col]&SCOREMASK; 788 if(scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 886 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} 905 final int scoreFromIns=packed[MODE_INS][row-1][col]&SCOREMASK; [all …]
|
H A D | SingleStateAlignerFlatFloat.java | 121 final float scoreFromIns=packed[row-1][col]; in fillUnlimited() 126 final float insScore=scoreFromIns+POINTS_INS;//*insWeights[rpos]; in fillUnlimited() 174 final float scoreFromIns=packed[row-1][col]; 179 final float insScore=scoreFromIns+POINTS_INS*insWeight; 202 final float scoreFromIns=packed[row-1][col]; in getState() local 207 final float insScore=scoreFromIns+POINTS_INS; in getState()
|
H A D | MultiStateAligner9PacBioAdapter3.java | 541 final int scoreFromIns=packed[MODE_INS][row-1][col-1]&SCOREMASK; in fillUnlimited() 550 int scoreI=scoreFromIns+POINTSoff_MATCH; in fillUnlimited() 588 int scoreI=scoreFromIns+POINTSoff_SUB; in fillUnlimited() 666 final int scoreFromIns=packed[MODE_INS][row-1][col]&SCOREMASK; in fillUnlimited() 670 int scoreI=scoreFromIns+insScoreArray[streak]; in fillUnlimited() 755 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} 793 final int scoreFromIns=packed[MODE_INS][row-1][col]&SCOREMASK; local 794 if(scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 892 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} in score() 911 final int scoreFromIns=packed[MODE_INS][row-1][col]&SCOREMASK; in score() local [all …]
|
H A D | MultiStateAligner9PacBioAdapter_WithBarriers.java | 633 int scoreI=scoreFromIns+POINTSoff_MATCH; in fillUnlimited() 672 int scoreI=scoreFromIns+POINTSoff_SUB; in fillUnlimited() 763 final int scoreFromIns=packed[MODE_INS][row-1][col]&SCOREMASK; in fillUnlimited() 767 int scoreI=scoreFromIns+(streak==0 ? POINTSoff_INS : in fillUnlimited() 860 int scoreI=scoreFromIns+POINTSoff_MATCH; 894 int scoreI=scoreFromIns+POINTSoff_SUB; 973 int scoreI=scoreFromIns+(streak==0 ? POINTSoff_INS : 1075 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} 1118 if(scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 1267 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} [all …]
|
H A D | SingleStateAlignerFlat2_1D.java | 104 final int scoreFromIns=get(row-1, col); in fillUnlimited() argument 109 final int insScore=scoreFromIns+POINTS_INS; in fillUnlimited() 152 final int scoreFromIns=get(row-1, col); 158 final int insScore=scoreFromIns+POINTS_INS;
|
H A D | SingleStateAlignerFlat2.java | 118 final int scoreFromIns=packed[row-1][col]; in fillUnlimited() 123 final int insScore=scoreFromIns+POINTS_INS; in fillUnlimited() 166 final int scoreFromIns=packed[row-1][col]; 172 final int insScore=scoreFromIns+POINTS_INS;
|
H A D | SingleStateAlignerFlat3.java | 118 final int scoreFromIns=packed[row-1][col]; in fillUnlimited() 123 final int insScore=scoreFromIns+POINTS_INS; in fillUnlimited() 166 final int scoreFromIns=packed[row-1][col]; 172 final int insScore=scoreFromIns+POINTS_INS;
|
H A D | SingleStateAlignerFlat2Amino.java | 117 final int scoreFromIns=packed[row-1][col]; in fillUnlimited() 122 final int insScore=scoreFromIns+POINTS_INS; in fillUnlimited() 165 final int scoreFromIns=packed[row-1][col]; 171 final int insScore=scoreFromIns+POINTS_INS;
|
H A D | SingleStateAlignerPacBioAdapter.java | 117 final int scoreFromIns=valueFromIns&HIGHMASK; in fillUnlimited() 133 final int insScore=scoreFromIns+insScoreArray[stateFromIns]; in fillUnlimited()
|
H A D | SingleStateAlignerFlat.java | 139 final int scoreFromIns=valueFromIns&HIGHMASK; in fillUnlimited() 155 final int insScore=scoreFromIns+POINTSoff_INS|MODE_INS; in fillUnlimited()
|
/dports/biology/bbmap/bbmap/current/align2/ |
H A D | MultiStateAligner11ts.java | 703 int scoreI=scoreFromIns+POINTSoff_MATCH; in fillUnlimited() 756 int scoreI=scoreFromIns+POINTSoff_SUB; in fillUnlimited() 858 final int scoreFromIns=packed[MODE_INS][row-1][col]&SCOREMASK; in fillUnlimited() local 862 int scoreI=scoreFromIns+POINTSoff_INS_ARRAY[streak+1]; in fillUnlimited() 958 int scoreI=scoreFromIns+POINTSoff_MATCH; in fillQ() 994 int scoreI=scoreFromIns+POINTSoff_SUB; in fillQ() 1073 int scoreI=scoreFromIns+POINTSoff_INS_ARRAY[streak+1]; in fillQ() 1176 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} 1219 if(scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 1373 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} [all …]
|
H A D | MultiStateAligner9XFlat.java | 656 int scoreI=scoreFromIns+POINTSoff_MATCH; in fillUnlimited() 694 int scoreI=scoreFromIns+POINTSoff_SUB; in fillUnlimited() 782 final int scoreFromIns=packed[MODE_INS][row-1][col]&SCOREMASK; in fillUnlimited() 786 int scoreI=scoreFromIns+(streak==0 ? POINTSoff_INS : in fillUnlimited() 879 int scoreI=scoreFromIns+POINTSoff_MATCH; 912 int scoreI=scoreFromIns+POINTSoff_SUB; 988 int scoreI=scoreFromIns+(streak==0 ? POINTSoff_INS : 1089 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} 1132 if(scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 1286 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} [all …]
|
H A D | MultiStateAligner9ts.java | 642 int scoreI=scoreFromIns+POINTSoff_MATCH; in fillUnlimited() 681 int scoreI=scoreFromIns+POINTSoff_SUB; in fillUnlimited() 772 final int scoreFromIns=packed[MODE_INS][row-1][col]&SCOREMASK; in fillUnlimited() 776 int scoreI=scoreFromIns+(streak==0 ? POINTSoff_INS : in fillUnlimited() 870 int scoreI=scoreFromIns+POINTSoff_MATCH; 904 int scoreI=scoreFromIns+POINTSoff_SUB; 983 int scoreI=scoreFromIns+(streak==0 ? POINTSoff_INS : 1085 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} 1128 if(scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 1281 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} [all …]
|
H A D | MultiStateAligner11tsJNI.java | 180 int scoreI=scoreFromIns+POINTSoff_MATCH; in fillQ() 207 int scoreI=scoreFromIns+POINTSoff_SUB; in fillQ() 272 …final int scoreFromIns=packed[(MODE_INS)*(maxRows+1)*(maxColumns+1)+(row-1)*(maxColumns+1)+(col)]&… in fillQ() 275 int scoreI=scoreFromIns+POINTSoff_INS_ARRAY[streak+1]; in fillQ() 358 if(scoreFromDiag>=scoreFromDel && scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 359 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} 400 …final int scoreFromIns=packed[(MODE_INS)*(maxRows+1)*(maxColumns+1)+(row-1)*(maxColumns+1)+(col)]&… 401 if(scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 546 if(scoreFromDiag>=scoreFromDel && scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 547 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} [all …]
|
H A D | MultiStateAligner9Flat.java | 662 int scoreI=scoreFromIns+POINTSoff_MATCH; in fillUnlimited() 701 int scoreI=scoreFromIns+POINTSoff_SUB; in fillUnlimited() 792 final int scoreFromIns=packed[MODE_INS][row-1][col]&SCOREMASK; in fillUnlimited() 796 int scoreI=scoreFromIns+(streak==0 ? POINTSoff_INS : in fillUnlimited() 890 int scoreI=scoreFromIns+POINTSoff_MATCH; 924 int scoreI=scoreFromIns+POINTSoff_SUB; 1003 int scoreI=scoreFromIns+(streak==0 ? POINTSoff_INS : 1105 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} 1148 if(scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 1302 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} [all …]
|
H A D | MultiStateAligner9PacBio.java | 662 int scoreI=scoreFromIns+POINTSoff_MATCH; in fillUnlimited() 701 int scoreI=scoreFromIns+POINTSoff_SUB; in fillUnlimited() 792 final int scoreFromIns=packed[MODE_INS][row-1][col]&SCOREMASK; in fillUnlimited() 796 int scoreI=scoreFromIns+(streak==0 ? POINTSoff_INS : in fillUnlimited() 890 int scoreI=scoreFromIns+POINTSoff_MATCH; 924 int scoreI=scoreFromIns+POINTSoff_SUB; 1003 int scoreI=scoreFromIns+(streak==0 ? POINTSoff_INS : 1105 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} 1148 if(scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 1302 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} [all …]
|
H A D | MultiStateAligner10ts.java | 1611 int scoreI=scoreFromIns+POINTSoff_MATCH; 1650 int scoreI=scoreFromIns+POINTSoff_SUB; 1741 final int scoreFromIns=packed[MODE_INS][row-1][col]&SCOREMASK; 1745 int scoreI=scoreFromIns+(streak==0 ? POINTSoff_INS : 1839 int scoreI=scoreFromIns+POINTSoff_MATCH; 1873 int scoreI=scoreFromIns+POINTSoff_SUB; 1952 int scoreI=scoreFromIns+(streak==0 ? POINTSoff_INS : 2056 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} 2099 if(scoreFromDiag>=scoreFromIns){prev=MODE_MS;} 2250 else if(scoreFromDel>=scoreFromIns){prev=MODE_DEL;} [all …]
|
/dports/biology/bbmap/bbmap/jni/ |
H A D | MultiStateAligner11tsJNI.c | 156 const jint scoreFromIns=packed[idxINS+tmp1+col-1]&SCOREMASK; in fillUnlimited() local 165 const jint scoreI=scoreFromIns+POINTSoff_MATCH; in fillUnlimited() 194 const jint scoreI=scoreFromIns+POINTSoff_SUB; in fillUnlimited() 268 const jint scoreFromIns=packed[idxINS+tmp1+col]&SCOREMASK; in fillUnlimited() local 271 const jint scoreI=scoreFromIns+POINTSoff_INS_ARRAY[streak+1]; in fillUnlimited()
|