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

/dports/biology/bbmap/bbmap/current/aligner/
H A DMultiStateAligner9PacBioAdapter2.java657 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 …]
H A DMultiStateAligner9PacBioAdapter.java584 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 …]
H A DMultiStateAligner9PacBioAdapter3.java584 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 …]
H A DMultiStateAligner9PacBioAdapter_WithBarriers.java668 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 …]
H A DSingleStateAlignerFlatFloat.java119 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()
H A DSingleStateAlignerFlat2_1D.java102 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);
H A DSingleStateAlignerFlat2.java116 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);
H A DSingleStateAlignerFlat3.java116 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);
H A DSingleStateAlignerFlat2Amino.java115 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);
H A DSingleStateAlignerPacBioAdapter.java113 final int scoreFromDiag=valueFromDiag&HIGHMASK; in fillUnlimited()
136 diagScore=scoreFromDiag+(rBase!='N' ? diagScore : POINTSoff_NOREF_MODE_SUB); in fillUnlimited()
H A DSingleStateAlignerFlat.java135 final int scoreFromDiag=valueFromDiag&HIGHMASK; in fillUnlimited()
158 diagScore=scoreFromDiag+(defined ? diagScore : POINTSoff_NOREF_MODE_SUB); in fillUnlimited()
/dports/biology/bbmap/bbmap/current/align2/
H A DMultiStateAligner11ts.java752 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 …]
H A DMultiStateAligner9XFlat.java690 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 …]
H A DMultiStateAligner9ts.java677 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 …]
H A DMultiStateAligner9Flat.java697 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 …]
H A DMultiStateAligner9PacBio.java697 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 …]
H A DMultiStateAligner11tsJNI.java178 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 …]
H A DMultiStateAligner10ts.java1646 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 …]
/dports/biology/bbmap/bbmap/jni/
H A DMultiStateAligner11tsJNI.c154 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()