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

/dports/biology/bbmap/bbmap/current/aligner/
H A DMultiStateAligner9PacBioAdapter2.java622 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 DMultiStateAligner9PacBioAdapter.java541 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;
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H A DSingleStateAlignerFlatFloat.java121 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 DMultiStateAligner9PacBioAdapter3.java541 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
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H A DMultiStateAligner9PacBioAdapter_WithBarriers.java633 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 DSingleStateAlignerFlat2_1D.java104 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 DSingleStateAlignerFlat2.java118 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 DSingleStateAlignerFlat3.java118 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 DSingleStateAlignerFlat2Amino.java117 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 DSingleStateAlignerPacBioAdapter.java117 final int scoreFromIns=valueFromIns&HIGHMASK; in fillUnlimited()
133 final int insScore=scoreFromIns+insScoreArray[stateFromIns]; in fillUnlimited()
H A DSingleStateAlignerFlat.java139 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 DMultiStateAligner11ts.java703 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;}
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H A DMultiStateAligner9XFlat.java656 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 DMultiStateAligner9ts.java642 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;}
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H A DMultiStateAligner11tsJNI.java180 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 DMultiStateAligner9Flat.java662 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 DMultiStateAligner9PacBio.java662 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 DMultiStateAligner10ts.java1611 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 DMultiStateAligner11tsJNI.c156 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()