dpScoutState (reference) in projects: dports

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Searched refs:dpScoutState (Results 1 – 24 of 24) sorted by relevance

/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align/
H A D	dp_setup.h	277 DPScoutState_<TDPScoutStateSpec> & dpScoutState, 287 …return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignC… 300 DPScoutState_<TDPScoutStateSpec> & dpScoutState, 308 …return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, al… 316 DPScoutState_<TDPScoutStateSpec> & dpScoutState, 323 …return _setUpAndRunAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig, … 339 DPScoutState_<TDPScoutStateSpec> & dpScoutState, 349 …return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignC… 358 DPScoutState_<TDPScoutStateSpec> & dpScoutState, 371 …return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, al… [all …]
H A D	align_interface_wrapper.h	88 DPScoutState_<Default> dpScoutState; in _alignWrapperSequential() 90 std::get<0>(tuple) = _setUpAndRunAlignment(traceSegments, dpScoutState, in _alignWrapperSequential() 128 DPScoutState_<Default> dpScoutState; in _alignWrapperSequential() 130 …std::get<0>(tuple) = _setUpAndRunAlignment(traceSegments, dpScoutState, stringH, std::get<1>(tuple… in _alignWrapperSequential() 172 DPScoutState_<Default> dpScoutState; in _alignWrapperSequential() 173 … std::get<0>(tuple) = _setUpAndRunAlignment(trace, dpScoutState, source(std::get<1>(tuple)), in _alignWrapperSequential()
H A D	local_alignment_unbanded.h	174 DPScoutState_<Default> dpScoutState; in localAlignment() local 175 …TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(row(align, 0)), source(row(ali… in localAlignment() 211 DPScoutState_<Default> dpScoutState; in localAlignment() local 212 …TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoring… in localAlignment() 250 DPScoutState_<Default> dpScoutState; in localAlignment() local 251 … TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, value(stringSet(alignmentGraph), 0), in localAlignment() 292 DPScoutState_<Default> dpScoutState; in localAlignment() local 293 …TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, value(strings, 0), value(strings, 1),… in localAlignment() 441 DPScoutState_<Default> dpScoutState; in SEQAN_FUNC_DISABLE_IF() local 443 …return _setUpAndRunAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, TAlignConfig2… in SEQAN_FUNC_DISABLE_IF()
H A D	local_alignment_banded.h	78 DPScoutState_<Default> dpScoutState; in localAlignment() local 79 …TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(row(align, 0)), source(row(ali… in localAlignment() 118 DPScoutState_<Default> dpScoutState; in localAlignment() local 119 …TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoring… in localAlignment() 158 DPScoutState_<Default> dpScoutState; in localAlignment() local 159 … TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, value(stringSet(alignmentGraph), 0), in localAlignment() 203 DPScoutState_<Default> dpScoutState; in localAlignment() local 204 …TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, value(strings, 0), value(strings, 1),… in localAlignment() 317 DPScoutState_<Default> dpScoutState; in SEQAN_FUNC_DISABLE_IF() local 319 return _setUpAndRunAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, in SEQAN_FUNC_DISABLE_IF()
H A D	global_alignment_banded.h	98 DPScoutState_<Default> dpScoutState; in globalAlignment() local 99 …TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(row(align, 0)), source(row(ali… in globalAlignment() 175 DPScoutState_<Default> dpScoutState; in globalAlignment() local 176 …TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoring… in globalAlignment() 257 DPScoutState_<Default> dpScoutState; in globalAlignment() local 258 … TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, value(stringSet(alignmentGraph), 0), in globalAlignment() 337 DPScoutState_<Default> dpScoutState; in globalAlignment() local 419 DPScoutState_<Default> dpScoutState; in SEQAN_FUNC_DISABLE_IF() local 421 return _setUpAndRunAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, in SEQAN_FUNC_DISABLE_IF() 495 DPScoutState_<Default> dpScoutState; in globalAlignmentScore() local [all …]
H A D	global_alignment_unbanded.h	189 DPScoutState_<Default> dpScoutState; in globalAlignment() local 190 …res = _setUpAndRunAlignment(trace, dpScoutState, source(row(align, 0)), source(row(align, 1)), sc… in globalAlignment() 257 DPScoutState_<Default> dpScoutState; in globalAlignment() local 258 …TScoreValue res = _setUpAndRunAlignment(traceSegments, dpScoutState, source(gapsH), source(gapsV),… in globalAlignment() 330 DPScoutState_<Default> dpScoutState; in globalAlignment() local 331 …TScoreValue res = _setUpAndRunAlignment(traceSegments, dpScoutState, value(stringSet(alignmentGrap… in globalAlignment() 401 DPScoutState_<Default> dpScoutState; in globalAlignment() local 402 …TScoreValue res = _setUpAndRunAlignment(traceSegments, dpScoutState, value(strings, 0), value(stri… in globalAlignment() 534 DPScoutState_<Default> dpScoutState; in SEQAN_FUNC_DISABLE_IF() local 601 DPScoutState_<Default> dpScoutState; in globalAlignmentScore() local [all …]
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align/
H A D	dp_setup.h	277 DPScoutState_<TDPScoutStateSpec> & dpScoutState, 287 …return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignC… 300 DPScoutState_<TDPScoutStateSpec> & dpScoutState, 308 …return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, al… 316 DPScoutState_<TDPScoutStateSpec> & dpScoutState, 323 …return _setUpAndRunAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig, … 339 DPScoutState_<TDPScoutStateSpec> & dpScoutState, 349 …return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignC… 358 DPScoutState_<TDPScoutStateSpec> & dpScoutState, 371 …return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, al… [all …]
H A D	align_interface_wrapper.h	88 DPScoutState_<Default> dpScoutState; in _alignWrapperSequential() 90 std::get<0>(tuple) = _setUpAndRunAlignment(traceSegments, dpScoutState, in _alignWrapperSequential() 128 DPScoutState_<Default> dpScoutState; in _alignWrapperSequential() 130 …std::get<0>(tuple) = _setUpAndRunAlignment(traceSegments, dpScoutState, stringH, std::get<1>(tuple… in _alignWrapperSequential() 172 DPScoutState_<Default> dpScoutState; in _alignWrapperSequential() 173 … std::get<0>(tuple) = _setUpAndRunAlignment(trace, dpScoutState, source(std::get<1>(tuple)), in _alignWrapperSequential()
H A D	local_alignment_unbanded.h	174 DPScoutState_<Default> dpScoutState; in localAlignment() local 175 …TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(row(align, 0)), source(row(ali… in localAlignment() 211 DPScoutState_<Default> dpScoutState; in localAlignment() local 212 …TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoring… in localAlignment() 250 DPScoutState_<Default> dpScoutState; in localAlignment() local 251 … TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, value(stringSet(alignmentGraph), 0), in localAlignment() 292 DPScoutState_<Default> dpScoutState; in localAlignment() local 293 …TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, value(strings, 0), value(strings, 1),… in localAlignment() 441 DPScoutState_<Default> dpScoutState; in SEQAN_FUNC_DISABLE_IF() local 443 …return _setUpAndRunAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, TAlignConfig2… in SEQAN_FUNC_DISABLE_IF()
H A D	local_alignment_banded.h	78 DPScoutState_<Default> dpScoutState; in localAlignment() local 79 …TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(row(align, 0)), source(row(ali… in localAlignment() 118 DPScoutState_<Default> dpScoutState; in localAlignment() local 119 …TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoring… in localAlignment() 158 DPScoutState_<Default> dpScoutState; in localAlignment() local 159 … TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, value(stringSet(alignmentGraph), 0), in localAlignment() 203 DPScoutState_<Default> dpScoutState; in localAlignment() local 204 …TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, value(strings, 0), value(strings, 1),… in localAlignment() 317 DPScoutState_<Default> dpScoutState; in SEQAN_FUNC_DISABLE_IF() local 319 return _setUpAndRunAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, in SEQAN_FUNC_DISABLE_IF()
H A D	global_alignment_banded.h	98 DPScoutState_<Default> dpScoutState; in globalAlignment() local 99 …TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(row(align, 0)), source(row(ali… in globalAlignment() 175 DPScoutState_<Default> dpScoutState; in globalAlignment() local 176 …TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoring… in globalAlignment() 257 DPScoutState_<Default> dpScoutState; in globalAlignment() local 258 … TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, value(stringSet(alignmentGraph), 0), in globalAlignment() 337 DPScoutState_<Default> dpScoutState; in globalAlignment() local 419 DPScoutState_<Default> dpScoutState; in SEQAN_FUNC_DISABLE_IF() local 421 return _setUpAndRunAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, in SEQAN_FUNC_DISABLE_IF() 495 DPScoutState_<Default> dpScoutState; in globalAlignmentScore() local [all …]
H A D	global_alignment_unbanded.h	189 DPScoutState_<Default> dpScoutState; in globalAlignment() local 190 …res = _setUpAndRunAlignment(trace, dpScoutState, source(row(align, 0)), source(row(align, 1)), sc… in globalAlignment() 257 DPScoutState_<Default> dpScoutState; in globalAlignment() local 258 …TScoreValue res = _setUpAndRunAlignment(traceSegments, dpScoutState, source(gapsH), source(gapsV),… in globalAlignment() 330 DPScoutState_<Default> dpScoutState; in globalAlignment() local 331 …TScoreValue res = _setUpAndRunAlignment(traceSegments, dpScoutState, value(stringSet(alignmentGrap… in globalAlignment() 401 DPScoutState_<Default> dpScoutState; in globalAlignment() local 402 …TScoreValue res = _setUpAndRunAlignment(traceSegments, dpScoutState, value(strings, 0), value(stri… in globalAlignment() 534 DPScoutState_<Default> dpScoutState; in SEQAN_FUNC_DISABLE_IF() local 601 DPScoutState_<Default> dpScoutState; in globalAlignmentScore() local [all …]
/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align/
H A D	dp_setup.h	272 DPScoutState_<TDPScoutStateSpec> & dpScoutState, 282 …return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignC… 292 DPScoutState_<TDPScoutStateSpec> & dpScoutState, 302 …return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignC… 312 DPScoutState_<TDPScoutStateSpec> & dpScoutState, 322 …return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignC… 331 DPScoutState_<TDPScoutStateSpec> & dpScoutState, 341 …return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, al… 346 …return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, al… 351 …return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, al… [all …]
H A D	local_alignment_unbanded.h	174 DPScoutState_<Default> dpScoutState; in localAlignment() local 175 …TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(row(align, 0)), source(row(ali… in localAlignment() 211 DPScoutState_<Default> dpScoutState; in localAlignment() local 212 …TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoring… in localAlignment() 250 DPScoutState_<Default> dpScoutState; in localAlignment() local 251 … TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, value(stringSet(alignmentGraph), 0), in localAlignment() 292 DPScoutState_<Default> dpScoutState; in localAlignment() local 293 …TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, value(strings, 0), value(strings, 1),… in localAlignment()
H A D	local_alignment_banded.h	78 DPScoutState_<Default> dpScoutState; in localAlignment() local 79 …TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(row(align, 0)), source(row(ali… in localAlignment() 118 DPScoutState_<Default> dpScoutState; in localAlignment() local 119 …TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoring… in localAlignment() 158 DPScoutState_<Default> dpScoutState; in localAlignment() local 159 … TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, value(stringSet(alignmentGraph), 0), in localAlignment() 203 DPScoutState_<Default> dpScoutState; in localAlignment() local 204 …TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, value(strings, 0), value(strings, 1),… in localAlignment()
H A D	global_alignment_banded.h	98 DPScoutState_<Default> dpScoutState; in globalAlignment() local 99 …TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(row(align, 0)), source(row(ali… in globalAlignment() 175 DPScoutState_<Default> dpScoutState; in globalAlignment() local 176 …TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoring… in globalAlignment() 257 DPScoutState_<Default> dpScoutState; in globalAlignment() local 258 … TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, value(stringSet(alignmentGraph), 0), in globalAlignment() 337 DPScoutState_<Default> dpScoutState; in globalAlignment() local 415 DPScoutState_<Default> dpScoutState; in globalAlignmentScore() local 417 return _setUpAndRunAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, in globalAlignmentScore() 491 DPScoutState_<Default> dpScoutState; in globalAlignmentScore() local [all …]
H A D	global_alignment_unbanded.h	189 DPScoutState_<Default> dpScoutState; in globalAlignment() local 190 …res = _setUpAndRunAlignment(trace, dpScoutState, source(row(align, 0)), source(row(align, 1)), sc… in globalAlignment() 257 DPScoutState_<Default> dpScoutState; in globalAlignment() local 258 …TScoreValue res = _setUpAndRunAlignment(traceSegments, dpScoutState, source(gapsH), source(gapsV),… in globalAlignment() 330 DPScoutState_<Default> dpScoutState; in globalAlignment() local 331 …TScoreValue res = _setUpAndRunAlignment(traceSegments, dpScoutState, value(stringSet(alignmentGrap… in globalAlignment() 401 DPScoutState_<Default> dpScoutState; in globalAlignment() local 402 …TScoreValue res = _setUpAndRunAlignment(traceSegments, dpScoutState, value(strings, 0), value(stri… in globalAlignment() 510 DPScoutState_<Default> dpScoutState; in globalAlignmentScore() local 577 DPScoutState_<Default> dpScoutState; in globalAlignmentScore() local [all …]
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/journaled_set/
H A D	journal_alignment_interface.h	`85 DPScoutState_<Default> dpScoutState; in globalAlignment() local 87 …TScoreValue res = _setUpAndRunAlignment(traceSegments, dpScoutState, reference, source, scoringSch… in globalAlignment() 178 DPScoutState_<Default> dpScoutState; in globalAlignment() local 180 …TScoreValue res = _setUpAndRunAlignment(traceSegments, dpScoutState, reference, source, scoringSch… in globalAlignment()`
/dports/biology/seqan/seqan-library-2.4.0/include/seqan/journaled_set/
H A D	journal_alignment_interface.h	`85 DPScoutState_<Default> dpScoutState; in globalAlignment() local 87 …TScoreValue res = _setUpAndRunAlignment(traceSegments, dpScoutState, reference, source, scoringSch… in globalAlignment() 178 DPScoutState_<Default> dpScoutState; in globalAlignment() local 180 …TScoreValue res = _setUpAndRunAlignment(traceSegments, dpScoutState, reference, source, scoringSch… in globalAlignment()`
/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/journaled_set/
H A D	journal_alignment_interface.h	`85 DPScoutState_<Default> dpScoutState; in globalAlignment() local 87 …TScoreValue res = _setUpAndRunAlignment(traceSegments, dpScoutState, reference, source, scoringSch… in globalAlignment() 178 DPScoutState_<Default> dpScoutState; in globalAlignment() local 180 …TScoreValue res = _setUpAndRunAlignment(traceSegments, dpScoutState, reference, source, scoringSch… in globalAlignment()`
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/yara/
H A D	find_verifier.h	`65 TDPState dpScoutState; member 114 me.dpScoutState, in verify()`
/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/seeds/
H A D	banded_chain_alignment_impl.h	1014 TDPScoutState & dpScoutState, in _finishBandedChain() argument 1035 …TGridPoint gridBegin(dpScoutState._horizontalNextGridOrigin, dpScoutState._verticalNextGridOrigin); in _finishBandedChain() 1056 …_reinitScoutState(dpScoutState, horizontalNextGridOrigin, verticalNextGridOrigin, length(infixH) +… in _finishBandedChain() 1062 …_computeAlignment(localTraceSet, dpScoutState, infixH, infixV, scoreSchemeGap, DPBandConfig<BandOf… in _finishBandedChain() 1086 _reinitScoutState(dpScoutState, 0, 0, upperDiagonal(band)+ 1, 1 - lowerDiagonal(band), in _finishBandedChain() 1091 …TScoreValue score = _computeAlignment(localTraceSet, dpScoutState, infixH, infixV, scoreSchemeAnch… in _finishBandedChain() 1119 …_reinitScoutState(dpScoutState, horizontalNextGridOrigin, verticalNextGridOrigin, upperDiagonal(ba… in _finishBandedChain() 1125 …TScoreValue score = _computeAlignment(localTraceSet, dpScoutState, infixH, infixV, scoreSchemeAnch… in _finishBandedChain() 1136 …_reinitScoutState(dpScoutState, 0, 0, length(seqH) - gridBegin.i1 + 1, length(seqV) - gridBegin.i2… in _finishBandedChain() 1141 …score = _computeAlignment(localTraceSet, dpScoutState, suffix(seqH, gridBegin.i1), suffix(seqV,gri… in _finishBandedChain()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/seeds/
H A D	banded_chain_alignment_impl.h	1108 TDPScoutState & dpScoutState, in _finishBandedChain() argument 1129 …TGridPoint gridBegin(dpScoutState._horizontalNextGridOrigin, dpScoutState._verticalNextGridOrigin); in _finishBandedChain() 1150 …_reinitScoutState(dpScoutState, horizontalNextGridOrigin, verticalNextGridOrigin, length(infixH) +… in _finishBandedChain() 1156 …_computeAlignment(localTraceSet, dpScoutState, infixH, infixV, scoreSchemeGap, DPBandConfig<BandOf… in _finishBandedChain() 1180 _reinitScoutState(dpScoutState, 0, 0, upperDiagonal(band)+ 1, 1 - lowerDiagonal(band), in _finishBandedChain() 1185 …TScoreValue score = _computeAlignment(localTraceSet, dpScoutState, infixH, infixV, scoreSchemeAnch… in _finishBandedChain() 1213 …_reinitScoutState(dpScoutState, horizontalNextGridOrigin, verticalNextGridOrigin, upperDiagonal(ba… in _finishBandedChain() 1219 …TScoreValue score = _computeAlignment(localTraceSet, dpScoutState, infixH, infixV, scoreSchemeAnch… in _finishBandedChain() 1230 …_reinitScoutState(dpScoutState, 0, 0, length(seqH) - gridBegin.i1 + 1, length(seqV) - gridBegin.i2… in _finishBandedChain() 1235 …score = _computeAlignment(localTraceSet, dpScoutState, suffix(seqH, gridBegin.i1), suffix(seqV,gri… in _finishBandedChain()
/dports/biology/seqan/seqan-library-2.4.0/include/seqan/seeds/
H A D	banded_chain_alignment_impl.h	1108 TDPScoutState & dpScoutState, in _finishBandedChain() argument 1129 …TGridPoint gridBegin(dpScoutState._horizontalNextGridOrigin, dpScoutState._verticalNextGridOrigin); in _finishBandedChain() 1150 …_reinitScoutState(dpScoutState, horizontalNextGridOrigin, verticalNextGridOrigin, length(infixH) +… in _finishBandedChain() 1156 …_computeAlignment(localTraceSet, dpScoutState, infixH, infixV, scoreSchemeGap, DPBandConfig<BandOf… in _finishBandedChain() 1180 _reinitScoutState(dpScoutState, 0, 0, upperDiagonal(band)+ 1, 1 - lowerDiagonal(band), in _finishBandedChain() 1185 …TScoreValue score = _computeAlignment(localTraceSet, dpScoutState, infixH, infixV, scoreSchemeAnch… in _finishBandedChain() 1213 …_reinitScoutState(dpScoutState, horizontalNextGridOrigin, verticalNextGridOrigin, upperDiagonal(ba… in _finishBandedChain() 1219 …TScoreValue score = _computeAlignment(localTraceSet, dpScoutState, infixH, infixV, scoreSchemeAnch… in _finishBandedChain() 1230 …_reinitScoutState(dpScoutState, 0, 0, length(seqH) - gridBegin.i1 + 1, length(seqV) - gridBegin.i2… in _finishBandedChain() 1235 …score = _computeAlignment(localTraceSet, dpScoutState, suffix(seqH, gridBegin.i1), suffix(seqV,gri… in _finishBandedChain()