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Searched refs:scoreFromDel (Results 1 – 19 of 19) sorted by relevance

/dports/biology/bbmap/bbmap/current/aligner/
H A DMultiStateAligner9PacBioAdapter2.java621 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;}
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H A DMultiStateAligner9PacBioAdapter.java540 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;
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H A DSingleStateAlignerFlatFloat.java120 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()
H A DMultiStateAligner9PacBioAdapter3.java540 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
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H A DMultiStateAligner9PacBioAdapter_WithBarriers.java632 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;}
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H A DSingleStateAlignerFlat2_1D.java103 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;
H A DSingleStateAlignerFlat2.java117 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;
H A DSingleStateAlignerFlat3.java117 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;
H A DSingleStateAlignerFlat2Amino.java116 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;
H A DSingleStateAlignerPacBioAdapter.java115 final int scoreFromDel=valueFromDel&HIGHMASK; in fillUnlimited()
132 final int delScore=scoreFromDel+delScoreArray[stateFromDel]; in fillUnlimited()
H A DSingleStateAlignerFlat.java137 final int scoreFromDel=valueFromDel&HIGHMASK; in fillUnlimited()
154 final int delScore=scoreFromDel+POINTSoff_DEL|MODE_DEL; in fillUnlimited()
/dports/biology/bbmap/bbmap/current/align2/
H A DMultiStateAligner11ts.java702 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;}
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H A DMultiStateAligner9XFlat.java655 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;}
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H A DMultiStateAligner9ts.java641 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;}
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H A DMultiStateAligner11tsJNI.java179 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 …]
H A DMultiStateAligner9Flat.java661 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 …]
H A DMultiStateAligner9PacBio.java661 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 …]
H A DMultiStateAligner10ts.java1610 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;}
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/dports/biology/bbmap/bbmap/jni/
H A DMultiStateAligner11tsJNI.c155 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()