diff --git a/.travis.yml b/.travis.yml index 0a76d6f99..6fcfccff7 100644 --- a/.travis.yml +++ b/.travis.yml @@ -42,7 +42,7 @@ before_install: install: - mkdir build && pushd build - - cmake -DCMAKE_BUILD_TYPE=Release -DOM_COPY_LIBS=1 .. + - cmake -DCMAKE_BUILD_TYPE=Release .. script: - make -j4 @@ -60,7 +60,6 @@ script: - echo "Using schema ../schema/$SCHEMA" - cp ../schema/$SCHEMA example/ - cp openMalaria example/ - - cp *.so example/ - pushd example && strip openMalaria && ./run-example-scenario.sh && popd - echo "Running test scenarios" - ctest -j4 diff --git a/appveyor.yml b/appveyor.yml index 7d6acc56e..1c0c88c16 100644 --- a/appveyor.yml +++ b/appveyor.yml @@ -33,6 +33,7 @@ after_build: - cmd: ECHO "build-log:" https://ci.appveyor.com/project/%APPVEYOR_ACCOUNT_NAME%/openmalaria/builds/%APPVEYOR_BUILD_ID% >> %APPVEYOR_BUILD_FOLDER%\OpenMalaria\appveyor.log - cmd: ECHO "build-version:" %APPVEYOR_BUILD_VERSION% >> %APPVEYOR_BUILD_FOLDER%\OpenMalaria\appveyor.log - cmd: ECHO "worker-image:" %APPVEYOR_BUILD_WORKER_IMAGE% >> %APPVEYOR_BUILD_FOLDER%\OpenMalaria\appveyor.log + - cmd: copy %APPVEYOR_BUILD_FOLDER%\version.txt %APPVEYOR_BUILD_FOLDER%\OpenMalaria - cmd: copy %APPVEYOR_BUILD_FOLDER%\xsd\bin\xerces-c*.dll %APPVEYOR_BUILD_FOLDER%\OpenMalaria - cmd: mkdir %APPVEYOR_BUILD_FOLDER%\OpenMalaria\schema - cmd: copy %APPVEYOR_BUILD_FOLDER%\schema\scenario_*.xsd %APPVEYOR_BUILD_FOLDER%\OpenMalaria\schema diff --git a/model/Transmission/NonVectorModel.cpp b/model/Transmission/NonVectorModel.cpp index aa30339cc..c52ec262f 100644 --- a/model/Transmission/NonVectorModel.cpp +++ b/model/Transmission/NonVectorModel.cpp @@ -217,7 +217,7 @@ void NonVectorModel::update () { } -double NonVectorModel::calculateEIR(Host::Human& human, double ageYears, vector& EIR){ +void NonVectorModel::calculateEIR(Host::Human& human, double ageYears, vector& EIR){ EIR.resize( 1 ); // no support for per-genotype tracking in this model (possible, but we're lazy) // where the full model, with estimates of human mosquito transmission is in use, use this: switch (simulationMode) { @@ -258,7 +258,10 @@ double NonVectorModel::calculateEIR(Host::Human& human, double ageYears, vector< } #endif EIR[0] *= human.perHostTransmission.relativeAvailabilityHetAge (ageYears); - return EIR[0]; + + auto ag = human.monAgeGroup().i(); + auto cs = human.cohortSet(); + mon::reportStatMACGF( mon::MVF_INOCS, ag, cs, 0, EIR[0] ); } diff --git a/model/Transmission/NonVectorModel.h b/model/Transmission/NonVectorModel.h index 7d31e6734..8fe30b4f9 100644 --- a/model/Transmission/NonVectorModel.h +++ b/model/Transmission/NonVectorModel.h @@ -73,7 +73,7 @@ class NonVectorModel : public TransmissionModel { virtual void vectorUpdate () {} virtual void update (); - virtual double calculateEIR(OM::Host::Human& human, double ageYears, vector< double >& EIR); + virtual void calculateEIR(OM::Host::Human& human, double ageYears, vector< double >& EIR); private: diff --git a/model/Transmission/TransmissionModel.cpp b/model/Transmission/TransmissionModel.cpp index 94727239f..52ba0c5e7 100644 --- a/model/Transmission/TransmissionModel.cpp +++ b/model/Transmission/TransmissionModel.cpp @@ -40,13 +40,6 @@ namespace OM { namespace Transmission { namespace vectors = util::vectors; -inline size_t survInocsSize(size_t nGenotypes){ - return mon::AgeGroup::numGroups() * mon::numCohortSets() * nGenotypes; } -inline size_t survInocsIndex(size_t ageGroup, size_t cohortSet, size_t genotype){ - return ageGroup + mon::AgeGroup::numGroups() * - (cohortSet + mon::numCohortSets() * genotype); -} - TransmissionModel* TransmissionModel::createTransmissionModel (const scnXml::Entomology& entoData, int populationSize) { // Entomology contains either a list of at least one anopheles or a list of at // least one EIRDaily. @@ -125,7 +118,6 @@ TransmissionModel::TransmissionModel(const scnXml::Entomology& entoData, tsNumAdults(0) { initialisationEIR.assign (SimTime::stepsPerYear(), 0.0); - surveyInoculations.assign(survInocsSize(nGenotypes), 0.0); using Monitoring::Continuous; Continuous.registerCallback( "input EIR", "\tinput EIR", MakeDelegate( this, &TransmissionModel::ctsCbInputEIR ) ); @@ -201,11 +193,6 @@ double TransmissionModel::getEIR( Host::Human& human, SimTime age, calculateEIR( human, ageYears, EIR ); util::streamValidate( EIR ); - for( size_t g = 0, nG = EIR.size(); g < nG; ++g ){ - size_t index = survInocsIndex(human.monAgeGroup().i(), human.cohortSet(), g); - surveyInoculations[index] += EIR[g]; - } - double allEIR = vectors::sum( EIR ); if( age >= adultAge ){ tsAdultEntoInocs += allEIR; @@ -220,19 +207,6 @@ void TransmissionModel::summarize () { if( !mon::isReported() ) return; // cannot use counters below when not reporting - for( size_t ag = 0, nAg = mon::AgeGroup::numGroups(), cs = 0, - nCS = mon::numCohortSets(), g = 0, nG = surveyInoculations.size() / (nAg * nCS); - ag < nAg; ++ag ) - { - for( cs = 0; cs < nCS; ++cs ){ - for( g = 0; g < nG; ++ g ){ - size_t index = survInocsIndex(ag, cs, g); - mon::reportStatMACGF( mon::MVF_INOCS, ag, cs, g, surveyInoculations[index] ); - } - } - } - surveyInoculations.assign( surveyInoculations.size(), 0.0 ); - double duration = (sim::now() - lastSurveyTime).inSteps(); if( duration == 0.0 ){ assert( surveyInputEIR == 0.0 && surveySimulatedEIR == 0.0 ); @@ -265,7 +239,6 @@ void TransmissionModel::checkpoint (istream& stream) { lastSurveyTime & stream; numTransmittingHumans & stream; tsNumAdults & stream; - surveyInoculations & stream; } void TransmissionModel::checkpoint (ostream& stream) { simulationMode & stream; @@ -283,7 +256,6 @@ void TransmissionModel::checkpoint (ostream& stream) { lastSurveyTime & stream; numTransmittingHumans & stream; tsNumAdults & stream; - surveyInoculations & stream; } } } diff --git a/model/Transmission/TransmissionModel.h b/model/Transmission/TransmissionModel.h index 18a0b7993..0761d36e7 100644 --- a/model/Transmission/TransmissionModel.h +++ b/model/Transmission/TransmissionModel.h @@ -215,7 +215,7 @@ class TransmissionModel { * @param EIR Out-vector. Set to the age- and heterogeneity-specific EIR an * individual human is exposed to, per parasite genotype, in units of * inoculations per day. Length set by callee. */ - virtual double calculateEIR(Host::Human& human, double ageYears, + virtual void calculateEIR(Host::Human& human, double ageYears, vector& EIR ) = 0; /** Needs to be called each time-step after Human::update() to update summary @@ -307,10 +307,6 @@ class TransmissionModel { /// accumulator for time step adults requesting EIR int tsNumAdults; - - /// Total inoculations since last survey (multidimensional). - /// See survInocsSize, survInocsIndex in cpp file. - vector surveyInoculations; }; } } diff --git a/model/Transmission/VectorModel.cpp b/model/Transmission/VectorModel.cpp index 8a23b2dba..04d4134fb 100644 --- a/model/Transmission/VectorModel.cpp +++ b/model/Transmission/VectorModel.cpp @@ -414,16 +414,18 @@ SimTime VectorModel::initIterate () { } } -double VectorModel::calculateEIR(Host::Human& human, double ageYears, +void VectorModel::calculateEIR(Host::Human& human, double ageYears, vector& EIR) { + auto ag = human.monAgeGroup().i(); + auto cs = human.cohortSet(); PerHost& host = human.perHostTransmission; host.update( human ); if (simulationMode == forcedEIR){ double eir = initialisationEIR[sim::ts0().moduloYearSteps()] * host.relativeAvailabilityHetAge (ageYears); + mon::reportStatMACGF( mon::MVF_INOCS, ag, cs, 0, eir ); EIR.assign( 1, eir ); - return eir; }else{ assert( simulationMode == dynamicEIR ); EIR.assign( WithinHost::Genotypes::N(), 0.0 ); @@ -441,10 +443,11 @@ double VectorModel::calculateEIR(Host::Human& human, double ageYears, * See comment in AnophelesModel::advancePeriod for method. */ double entoFactor = ageFactor * host.availBite(species[i].getHumanBaseParams(), i); for( size_t g = 0; g < EIR.size(); ++g ){ - EIR[g] += partialEIR[g] * entoFactor; + auto eir = partialEIR[g] * entoFactor; + mon::reportStatMACSGF( mon::MVF_INOCS, ag, cs, i, g, eir ); + EIR[g] += eir; } } - return vectors::sum( EIR ); } } diff --git a/model/Transmission/VectorModel.h b/model/Transmission/VectorModel.h index ae8d23130..baaac7312 100644 --- a/model/Transmission/VectorModel.h +++ b/model/Transmission/VectorModel.h @@ -62,7 +62,7 @@ class VectorModel : public TransmissionModel { virtual void vectorUpdate (); virtual void update (); - virtual double calculateEIR( Host::Human& human, double ageYears, + virtual void calculateEIR( Host::Human& human, double ageYears, vector& EIR ); virtual const map& getSpeciesIndexMap(); diff --git a/model/mon/OutputMeasures.h b/model/mon/OutputMeasures.h index ff1f35c41..6f7811d79 100644 --- a/model/mon/OutputMeasures.h +++ b/model/mon/OutputMeasures.h @@ -236,8 +236,8 @@ void defineOutMeasures(){ /// Kappa (human infectiousness) weighted by availability per day-of-year for the last year. /// (Reporting removed.) namedOutMeasures["kappaPerDayOfYear"] = OutMeasure::obsolete( 29 ); - /** The total number of inoculations, by age group and cohort, summed over - * the reporting period. */ + /** The total number of inoculations, by age group, cohort and parasite + * genotype, summed over the reporting period. */ namedOutMeasures["innoculationsPerAgeGroup"] = OutMeasure::humanACG( 30, MVF_INOCS, true ); /// N_v0: emergence of feeding vectors during the last time step. Units: mosquitoes/day @@ -450,6 +450,10 @@ void defineOutMeasures(){ */ namedOutMeasures["expectedSevere"] = OutMeasure::humanAC( 78, MHF_EXPECTED_SEVERE, true ); + /** The total number of inoculations, by mosquito species, summed over + * the reporting period. */ + namedOutMeasures["innoculationsPerVector"] = + OutMeasure::species( 79, MVF_INOCS, false ); // Now initialise valid condition measures: foreach( const NamedMeasureMapT::value_type& v, namedOutMeasures ){ diff --git a/model/mon/mon.cpp b/model/mon/mon.cpp index 035b89ca0..959534e18 100644 --- a/model/mon/mon.cpp +++ b/model/mon/mon.cpp @@ -655,6 +655,12 @@ void reportStatMACGF( Measure measure, size_t ageIndex, uint32_t cohortSet, const size_t survey = impl::survNumStat; storeF.report( val, measure, survey, ageIndex, cohortSet, 0, genotype, 0 ); } +void reportStatMACSGF( Measure measure, size_t ageIndex, uint32_t cohortSet, + size_t species, size_t genotype, double val ) +{ + const size_t survey = impl::survNumStat; + storeF.report( val, measure, survey, ageIndex, cohortSet, species, genotype, 0 ); +} void reportStatMHPF( Measure measure, const Host::Human& human, size_t drug, double val ){ const size_t survey = impl::survNumStat; const size_t ageIndex = human.monAgeGroup().i(); diff --git a/model/mon/reporting.h b/model/mon/reporting.h index aaefc6a37..2398df7c2 100644 --- a/model/mon/reporting.h +++ b/model/mon/reporting.h @@ -227,7 +227,7 @@ void reportStatMHF( Measure measure, const Host::Human& human, double val ); /// Report some value (floating point) for the current survey and some age /// group and cohort set void reportStatMACGF( Measure measure, size_t ageIndex, uint32_t cohortSet, - size_t genotpye, double val ); + size_t genotype, double val ); /// Report some value (floating point) for some human and genotype to the current survey. void reportStatMHGF( Measure measure, const Host::Human& human, size_t genotype, double val ); @@ -237,6 +237,10 @@ void reportStatMHPF( Measure measure, const Host::Human& human, size_t drugIndex void reportStatMSF( Measure measure, size_t species, double val ); /// Report some value (floating point) by genotype to the current survey. void reportStatMSGF( Measure measure, size_t species, size_t genotype, double val ); +/// Report some value (floating point) for the current survey and some age +/// group, cohort set, genotype and vector species +void reportStatMACSGF( Measure measure, size_t ageIndex, uint32_t cohortSet, + size_t species, size_t genotype, double val ); /// Query whether an output measure is used. /// This function is not fast, so it is recommended to cache the result. diff --git a/test/expected/outputGenotypes.txt b/test/expected/outputGenotypes.txt index 7c5b6570f..e6c612b90 100644 --- a/test/expected/outputGenotypes.txt +++ b/test/expected/outputGenotypes.txt @@ -167,6 +167,9 @@ 1 1000009 73 0 1 1000010 73 0 1 1000011 73 0 +1 1 79 0.888462 +1 2 79 0.010307 +1 3 79 7.36426 1 0 169 68 1 1000000 169 60 1 0 170 13 @@ -342,6 +345,9 @@ 2 1000009 73 0 2 1000010 73 0 2 1000011 73 0 +2 1 79 12422.8 +2 2 79 1479.62 +2 3 79 103134 2 0 169 573 2 1000000 169 477 2 0 170 307 @@ -517,6 +523,9 @@ 3 1000009 73 0 3 1000010 73 0 3 1000011 73 0 +3 1 79 6369.47 +3 2 79 151588 +3 3 79 53703.4 3 0 169 520 3 1000000 169 466 3 0 170 352 @@ -692,6 +701,9 @@ 4 1000009 73 0 4 1000010 73 0 4 1000011 73 0 +4 1 79 597.853 +4 2 79 26752.7 +4 3 79 5026.52 4 0 169 202 4 1000000 169 172 4 0 170 127 @@ -867,6 +879,9 @@ 5 1000009 73 0 5 1000010 73 0 5 1000011 73 0 +5 1 79 51.2278 +5 2 79 27.6674 +5 3 79 429.816 5 0 169 64 5 1000000 169 44 5 0 170 10 @@ -1042,6 +1057,9 @@ 6 1000009 73 0 6 1000010 73 0 6 1000011 73 0 +6 1 79 11245.7 +6 2 79 1227.44 +6 3 79 93346.5 6 0 169 584 6 1000000 169 448 6 0 170 344 @@ -1217,6 +1235,9 @@ 7 1000009 73 0 7 1000010 73 0 7 1000011 73 0 +7 1 79 5469.72 +7 2 79 145183 +7 3 79 46011.3 7 0 169 558 7 1000000 169 432 7 0 170 359 @@ -1392,6 +1413,9 @@ 8 1000009 73 0 8 1000010 73 0 8 1000011 73 0 +8 1 79 602.746 +8 2 79 26189.9 +8 3 79 5067.74 8 0 169 219 8 1000000 169 164 8 0 170 154 @@ -1567,6 +1591,9 @@ 9 1000009 73 0 9 1000010 73 0 9 1000011 73 0 +9 1 79 50.9376 +9 2 79 28.8408 +9 3 79 427.858 9 0 169 55 9 1000000 169 55 9 0 170 13 @@ -1742,6 +1769,9 @@ 10 1000009 73 0 10 1000010 73 0 10 1000011 73 0 +10 1 79 13632.8 +10 2 79 1319.24 +10 3 79 113230 10 0 169 616 10 1000000 169 473 10 0 170 386 @@ -1917,6 +1947,9 @@ 11 1000009 73 0 11 1000010 73 0 11 1000011 73 0 +11 1 79 5901.5 +11 2 79 152921 +11 3 79 49723.7 11 0 169 558 11 1000000 169 400 11 0 170 386 @@ -2092,6 +2125,9 @@ 12 1000009 73 0 12 1000010 73 0 12 1000011 73 0 +12 1 79 591.363 +12 2 79 25928.7 +12 3 79 4970.93 12 0 169 225 12 1000000 169 173 12 0 170 154 @@ -2267,6 +2303,9 @@ 13 1000009 73 0 13 1000010 73 0 13 1000011 73 0 +13 1 79 54.3771 +13 2 79 30.1662 +13 3 79 456.7 13 0 169 71 13 1000000 169 49 13 0 170 17 @@ -2442,6 +2481,9 @@ 14 1000009 73 0 14 1000010 73 0 14 1000011 73 0 +14 1 79 13007.2 +14 2 79 1383.06 +14 3 79 108011 14 0 169 611 14 1000000 169 491 14 0 170 382 @@ -2617,6 +2659,9 @@ 15 1000009 73 0 15 1000010 73 0 15 1000011 73 0 +15 1 79 6012.35 +15 2 79 151229 +15 3 79 50665.2 15 0 169 550 15 1000000 169 413 15 0 170 351 @@ -2792,6 +2837,9 @@ 16 1000009 73 0 16 1000010 73 0 16 1000011 73 0 +16 1 79 590.695 +16 2 79 26285.7 +16 3 79 4965.28 16 0 169 207 16 1000000 169 177 16 0 170 153 @@ -2967,6 +3015,9 @@ 17 1000009 73 0 17 1000010 73 0 17 1000011 73 0 +17 1 79 48.7865 +17 2 79 27.3124 +17 3 79 409.546 17 0 169 70 17 1000000 169 62 17 0 170 12 @@ -3142,6 +3193,9 @@ 18 1000009 73 0 18 1000010 73 0 18 1000011 73 0 +18 1 79 11975 +18 2 79 1283.12 +18 3 79 99407.1 18 0 169 457 18 1000000 169 576 18 0 170 267 @@ -3317,6 +3371,9 @@ 19 1000009 73 0 19 1000010 73 0 19 1000011 73 0 +19 1 79 5709.2 +19 2 79 148990 +19 3 79 48058.2 19 0 169 421 19 1000000 169 515 19 0 170 277 @@ -3492,6 +3549,9 @@ 20 1000009 73 0 20 1000010 73 0 20 1000011 73 0 +20 1 79 591.865 +20 2 79 26760.3 +20 3 79 4975.07 20 0 169 160 20 1000000 169 218 20 0 170 101 @@ -3667,6 +3727,9 @@ 21 1000009 73 0 21 1000010 73 0 21 1000011 73 0 +21 1 79 50.5424 +21 2 79 28.4143 +21 3 79 424.232 21 0 169 38 21 1000000 169 81 21 0 170 11 @@ -3842,6 +3905,9 @@ 22 1000009 73 0 22 1000010 73 0 22 1000011 73 0 +22 1 79 11612 +22 2 79 1340.21 +22 3 79 96400.6 22 0 169 445 22 1000000 169 578 22 0 170 250 @@ -4017,6 +4083,9 @@ 23 1000009 73 0 23 1000010 73 0 23 1000011 73 0 +23 1 79 5684.17 +23 2 79 145295 +23 3 79 47832.2 23 0 169 428 23 1000000 169 539 23 0 170 263 @@ -4192,6 +4261,9 @@ 24 1000009 73 0 24 1000010 73 0 24 1000011 73 0 +24 1 79 580.015 +24 2 79 25956.8 +24 3 79 4873.43 24 0 169 145 24 1000000 169 205 24 0 170 93 @@ -4367,6 +4439,9 @@ 25 1000009 73 0 25 1000010 73 0 25 1000011 73 0 +25 1 79 47.7709 +25 2 79 26.9729 +25 3 79 400.945 25 0 169 44 25 1000000 169 64 25 0 170 4 @@ -4542,6 +4617,9 @@ 26 1000009 73 0 26 1000010 73 0 26 1000011 73 0 +26 1 79 9573.44 +26 2 79 1089.39 +26 3 79 79441 26 0 169 440 26 1000000 169 518 26 0 170 243 @@ -4717,6 +4795,9 @@ 27 1000009 73 0 27 1000010 73 0 27 1000011 73 0 +27 1 79 4972.75 +27 2 79 138979 +27 3 79 41761.5 27 0 169 433 27 1000000 169 501 27 0 170 287 @@ -4892,6 +4973,9 @@ 28 1000009 73 0 28 1000010 73 0 28 1000011 73 0 +28 1 79 571.67 +28 2 79 25427.1 +28 3 79 4802.8 28 0 169 172 28 1000000 169 215 28 0 170 119 @@ -5067,6 +5151,9 @@ 29 1000009 73 0 29 1000010 73 0 29 1000011 73 0 +29 1 79 52.3217 +29 2 79 28.6727 +29 3 79 439.076 29 0 169 43 29 1000000 169 67 29 0 170 8 @@ -5242,6 +5329,9 @@ 30 1000009 73 0 30 1000010 73 0 30 1000011 73 0 +30 1 79 9903.92 +30 2 79 1094.5 +30 3 79 82169.2 30 0 169 387 30 1000000 169 540 30 0 170 227 @@ -5417,6 +5507,9 @@ 31 1000009 73 0 31 1000010 73 0 31 1000011 73 0 +31 1 79 5238.45 +31 2 79 138081 +31 3 79 44018.6 31 0 169 384 31 1000000 169 544 31 0 170 245 @@ -5592,6 +5685,9 @@ 32 1000009 73 0 32 1000010 73 0 32 1000011 73 0 +32 1 79 572.072 +32 2 79 25875.4 +32 3 79 4805.45 32 0 169 135 32 1000000 169 212 32 0 170 94 @@ -5767,6 +5863,9 @@ 33 1000009 73 0 33 1000010 73 0 33 1000011 73 0 +33 1 79 47.1116 +33 2 79 26.8472 +33 3 79 395.193 33 0 169 30 33 1000000 169 63 33 0 170 7 @@ -5942,6 +6041,9 @@ 34 1000009 73 -11.4602 34 1000010 73 -16.4529 34 1000011 73 -8.62616 +34 1 79 7706.91 +34 2 79 886.147 +34 3 79 63907.7 34 0 169 332 34 1000000 169 587 34 0 170 138 @@ -6117,6 +6219,9 @@ 35 1000009 73 -125.043 35 1000010 73 -101.135 35 1000011 73 -41.9213 +35 1 79 4213.02 +35 2 79 97811.9 +35 3 79 35268.1 35 0 169 161 35 1000000 169 684 35 0 170 56 @@ -6292,6 +6397,9 @@ 36 1000009 73 -161.105 36 1000010 73 -135.059 36 1000011 73 -63.3333 +36 1 79 352.254 +36 2 79 16543.9 +36 3 79 2942.58 36 0 169 38 36 1000000 169 374 36 0 170 15 @@ -6467,6 +6575,9 @@ 37 1000009 73 -207.095 37 1000010 73 -165.088 37 1000011 73 -61.2776 +37 1 79 41.4319 +37 2 79 22.2054 +37 3 79 345.893 37 0 169 12 37 1000000 169 140 37 0 170 2 @@ -6642,6 +6753,9 @@ 38 1000009 73 -149.123 38 1000010 73 -96.0171 38 1000011 73 -54.2304 +38 1 79 11131.8 +38 2 79 1260.51 +38 3 79 92401.6 38 0 169 84 38 1000000 169 818 38 0 170 18 @@ -6817,6 +6931,9 @@ 39 1000009 73 -127.203 39 1000010 73 -110.676 39 1000011 73 -46.4686 +39 1 79 5055.24 +39 2 79 111743 +39 3 79 42431.4 39 0 169 33 39 1000000 169 770 39 0 170 6 @@ -6992,6 +7109,9 @@ 40 1000009 73 -166.416 40 1000010 73 -148.524 40 1000011 73 -66.8551 +40 1 79 403.846 +40 2 79 17814.2 +40 3 79 3378.13 40 0 169 1 40 1000000 169 411 40 0 170 1 @@ -7167,6 +7287,9 @@ 41 1000009 73 -214.768 41 1000010 73 -172.346 41 1000011 73 -72.3626 +41 1 79 47.8309 +41 2 79 22.6301 +41 3 79 399.391 41 0 169 0 41 1000000 169 184 41 0 170 0 @@ -7342,6 +7465,9 @@ 42 1000009 73 -143.655 42 1000010 73 -106.377 42 1000011 73 -23.1783 +42 1 79 12814.1 +42 2 79 1324.68 +42 3 79 106382 42 0 169 0 42 1000000 169 854 42 0 170 0 @@ -7517,6 +7643,9 @@ 43 1000009 73 -165.105 43 1000010 73 -84.66 43 1000011 73 -54.4307 +43 1 79 5577.22 +43 2 79 115691 +43 3 79 46894.3 43 0 169 0 43 1000000 169 804 43 0 170 0 @@ -7692,6 +7821,9 @@ 44 1000009 73 -202.424 44 1000010 73 -123.521 44 1000011 73 -74.7409 +44 1 79 403.182 +44 2 79 18401 +44 3 79 3372.91 44 0 169 0 44 1000000 169 415 44 0 170 0 @@ -7867,6 +7999,9 @@ 45 1000009 73 -301.339 45 1000010 73 -138.088 45 1000011 73 -80.9672 +45 1 79 45.673 +45 2 79 22.85 +45 3 79 381.525 45 0 169 0 45 1000000 169 178 45 0 170 0 @@ -8042,6 +8177,9 @@ 46 1000009 73 -174.174 46 1000010 73 -72.2181 46 1000011 73 -46.4798 +46 1 79 11412.8 +46 2 79 1244.8 +46 3 79 94742.5 46 0 169 0 46 1000000 169 807 46 0 170 0 @@ -8217,6 +8355,9 @@ 47 1000009 73 -190.879 47 1000010 73 -86.5893 47 1000011 73 -42.7036 +47 1 79 5176.38 +47 2 79 109122 +47 3 79 43461.9 47 0 169 0 47 1000000 169 787 47 0 170 0 @@ -8392,6 +8533,9 @@ 48 1000009 73 -242.565 48 1000010 73 -102.486 48 1000011 73 -56.4372 +48 1 79 397.643 +48 2 79 17676.4 +48 3 79 3325.97 48 0 169 0 48 1000000 169 419 48 0 170 0 @@ -8567,6 +8711,9 @@ 49 1000009 73 -355.634 49 1000010 73 -116.589 49 1000011 73 -73.6665 +49 1 79 48.0135 +49 2 79 23.6124 +49 3 79 401.019 49 0 169 0 49 1000000 169 172 49 0 170 0 @@ -8742,6 +8889,9 @@ 50 1000009 73 -208.378 50 1000010 73 -87.3298 50 1000011 73 -40.6343 +50 1 79 13419.3 +50 2 79 1290.42 +50 3 79 111441 50 0 169 0 50 1000000 169 854 50 0 170 0 @@ -8917,6 +9067,9 @@ 51 1000009 73 -205.073 51 1000010 73 -67.9886 51 1000011 73 -59.1733 +51 1 79 5402.53 +51 2 79 115532 +51 3 79 45409.8 51 0 169 0 51 1000000 169 798 51 0 170 0 @@ -9092,6 +9245,9 @@ 52 1000009 73 -255.165 52 1000010 73 -77.2386 52 1000011 73 -79.5807 +52 1 79 422.077 +52 2 79 19113.5 +52 3 79 3532.58 52 0 169 0 52 1000000 169 411 52 0 170 0 @@ -9267,6 +9423,9 @@ 53 1000009 73 -333.082 53 1000010 73 -99.7275 53 1000011 73 -102.229 +53 1 79 44.0429 +53 2 79 23.7988 +53 3 79 368.198 53 0 169 0 53 1000000 169 178 53 0 170 0 @@ -9442,6 +9601,9 @@ 54 1000009 73 -188.409 54 1000010 73 -79.188 54 1000011 73 -48.6837 +54 1 79 11268.6 +54 2 79 1145.38 +54 3 79 93516.9 54 0 169 0 54 1000000 169 825 54 0 170 0 @@ -9617,6 +9779,9 @@ 55 1000009 73 -185.346 55 1000010 73 -62.7674 55 1000011 73 -61.1103 +55 1 79 4993.67 +55 2 79 110626 +55 3 79 41917.1 55 0 169 0 55 1000000 169 796 55 0 170 0 @@ -9792,6 +9957,9 @@ 56 1000009 73 -250.59 56 1000010 73 -80.8835 56 1000011 73 -80.8474 +56 1 79 399.489 +56 2 79 18679.1 +56 3 79 3341.64 56 0 169 0 56 1000000 169 431 56 0 170 0 @@ -9967,6 +10135,9 @@ 57 1000009 73 -285.606 57 1000010 73 -100.554 57 1000011 73 -114.297 +57 1 79 47.8513 +57 2 79 25.3924 +57 3 79 400.09 57 0 169 0 57 1000000 169 175 57 0 170 0 @@ -10142,6 +10313,9 @@ 58 1000009 73 -191.99 58 1000010 73 -43.5073 58 1000011 73 -68.5233 +58 1 79 12199.5 +58 2 79 1192.57 +58 3 79 101271 58 0 169 0 58 1000000 169 833 58 0 170 0 @@ -10317,6 +10491,9 @@ 59 1000009 73 -186.815 59 1000010 73 -47.2441 59 1000011 73 -52.1254 +59 1 79 5225.9 +59 2 79 113518 +59 3 79 43897.6 59 0 169 0 59 1000000 169 796 59 0 170 0 @@ -10492,6 +10669,9 @@ 60 1000009 73 -232.464 60 1000010 73 -75.8691 60 1000011 73 -60.8182 +60 1 79 424.645 +60 2 79 18988.8 +60 3 79 3554.05 60 0 169 0 60 1000000 169 436 60 0 170 0 @@ -10667,6 +10847,9 @@ 61 1000009 73 -297.968 61 1000010 73 -118.455 61 1000011 73 -91.6606 +61 1 79 47.7204 +61 2 79 22.425 +61 3 79 398.395 61 0 169 0 61 1000000 169 192 61 0 170 0 @@ -10842,6 +11025,9 @@ 62 1000009 73 -198.216 62 1000010 73 -70.6702 62 1000011 73 -75.4998 +62 1 79 12370.7 +62 2 79 1216.5 +62 3 79 102703 62 0 169 0 62 1000000 169 843 62 0 170 0 @@ -11017,6 +11203,9 @@ 63 1000009 73 -153.766 63 1000010 73 -82.8308 63 1000011 73 -47.3301 +63 1 79 5242.44 +63 2 79 114548 +63 3 79 44045.4 63 0 169 0 63 1000000 169 796 63 0 170 0 @@ -11192,6 +11381,9 @@ 64 1000009 73 -203.058 64 1000010 73 -106.193 64 1000011 73 -72.5598 +64 1 79 415.341 +64 2 79 18788 +64 3 79 3475.32 64 0 169 0 64 1000000 169 437 64 0 170 0 @@ -11367,6 +11559,9 @@ 65 1000009 73 -281.043 65 1000010 73 -89.8404 65 1000011 73 -78.7432 +65 1 79 44.6106 +65 2 79 22.7578 +65 3 79 372.724 65 0 169 0 65 1000000 169 161 65 0 170 0 @@ -11542,6 +11737,9 @@ 66 1000009 73 -212.156 66 1000010 73 -102.169 66 1000011 73 -53.619 +66 1 79 11703.9 +66 2 79 1125.14 +66 3 79 97150.5 66 0 169 0 66 1000000 169 837 66 0 170 0 @@ -11717,6 +11915,9 @@ 67 1000009 73 -174.318 67 1000010 73 -92.8285 67 1000011 73 -54.4113 +67 1 79 5083.34 +67 2 79 110361 +67 3 79 42681.7 67 0 169 0 67 1000000 169 776 67 0 170 0 @@ -11892,6 +12093,9 @@ 68 1000009 73 -221.949 68 1000010 73 -117.121 68 1000011 73 -55.7398 +68 1 79 401.042 +68 2 79 17858.3 +68 3 79 3354.03 68 0 169 0 68 1000000 169 423 68 0 170 0 @@ -12067,6 +12271,9 @@ 69 1000009 73 -282.071 69 1000010 73 -156.302 69 1000011 73 -86.5639 +69 1 79 49.8993 +69 2 79 22.7962 +69 3 79 416.467 69 0 169 0 69 1000000 169 190 69 0 170 0 @@ -12242,6 +12449,9 @@ 70 1000009 73 -170.201 70 1000010 73 -105.016 70 1000011 73 -73.7162 +70 1 79 14918.5 +70 2 79 1331.95 +70 3 79 123897 70 0 169 0 70 1000000 169 884 70 0 170 0 @@ -12417,6 +12627,9 @@ 71 1000009 73 -193.656 71 1000010 73 -97.461 71 1000011 73 -66.3521 +71 1 79 5772.38 +71 2 79 116885 +71 3 79 48578 71 0 169 0 71 1000000 169 780 71 0 170 0 @@ -12592,6 +12805,9 @@ 72 1000009 73 -240.533 72 1000010 73 -127.106 72 1000011 73 -83.7359 +72 1 79 422.703 +72 2 79 18207.7 +72 3 79 3537.7 72 0 169 0 72 1000000 169 431 72 0 170 0 @@ -12767,6 +12983,9 @@ 73 1000009 73 -289.26 73 1000010 73 -152.814 73 1000011 73 -95.3591 +73 1 79 46.5154 +73 2 79 22.4188 +73 3 79 388.432 73 0 169 0 73 1000000 169 183 73 0 170 0 @@ -12942,6 +13161,9 @@ 74 1000009 73 -166.957 74 1000010 73 -70.9707 74 1000011 73 -66.262 +74 1 79 12141.6 +74 2 79 1343.62 +74 3 79 100783 74 0 169 0 74 1000000 169 845 74 0 170 0 @@ -13117,6 +13339,9 @@ 75 1000009 73 -183.028 75 1000010 73 -107.416 75 1000011 73 -67.7904 +75 1 79 5511.55 +75 2 79 113114 +75 3 79 46319.2 75 0 169 0 75 1000000 169 790 75 0 170 0 @@ -13292,6 +13517,9 @@ 76 1000009 73 -214.735 76 1000010 73 -132.217 76 1000011 73 -84.4313 +76 1 79 400.076 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--git a/test/expected/outputVecFullTest.txt b/test/expected/outputVecFullTest.txt index 28d414783..2a8dad63b 100644 --- a/test/expected/outputVecFullTest.txt +++ b/test/expected/outputVecFullTest.txt @@ -179,6 +179,9 @@ 1 9 59 0 1 10 59 0 1 11 59 0 +1 1 79 3.91425 +1 2 79 0.0411603 +1 3 79 32.6625 2 1 0 11 2 2 0 5 2 3 0 12 @@ -360,6 +363,9 @@ 2 9 59 0 2 10 59 0 2 11 59 0 +2 1 79 382.386 +2 2 79 1.64748 +2 3 79 3284.32 3 1 0 10 3 2 0 5 3 3 0 13 @@ -541,6 +547,9 @@ 3 9 59 0 3 10 59 0 3 11 59 0 +3 1 79 1.31669 +3 2 79 24.5161 +3 3 79 37.7588 4 1 0 6 4 2 0 9 4 3 0 12 @@ -722,6 +731,9 @@ 4 9 59 0 4 10 59 0 4 11 59 0 +4 1 79 0.268492 +4 2 79 2.22551 +4 3 79 3.83256 5 1 0 8 5 2 0 7 5 3 0 12 @@ -903,6 +915,9 @@ 5 9 59 0 5 10 59 0 5 11 59 0 +5 1 79 0.0429773 +5 2 79 0 +5 3 79 0.493814 6 1 0 9 6 2 0 8 6 3 0 11 @@ -1084,6 +1099,9 @@ 6 9 59 0 6 10 59 0 6 11 59 0 +6 1 79 9.18214 +6 2 79 0.393477 +6 3 79 93.5412 7 1 0 9 7 2 0 7 7 3 0 11 @@ -1265,6 +1283,9 @@ 7 9 59 0 7 10 59 0 7 11 59 0 +7 1 79 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1 79 329.575 +67 2 79 5658.22 +67 3 79 3297.91 68 1 0 7 68 2 0 8 68 3 0 13 @@ -12306,6 +12507,9 @@ 68 9 59 0 68 10 59 0 68 11 59 0 +68 1 79 23.2385 +68 2 79 996.533 +68 3 79 214.175 69 1 0 9 69 2 0 7 69 3 0 14 @@ -12487,6 +12691,9 @@ 69 9 59 0 69 10 59 0 69 11 59 0 +69 1 79 5.54277 +69 2 79 1.76613 +69 3 79 51.5464 70 1 0 8 70 2 0 8 70 3 0 14 @@ -12668,6 +12875,9 @@ 70 9 59 0 70 10 59 0 70 11 59 0 +70 1 79 1787.99 +70 2 79 118.019 +70 3 79 16866.7 71 1 0 9 71 2 0 8 71 3 0 15 @@ -12849,6 +13059,9 @@ 71 9 59 0 71 10 59 0 71 11 59 0 +71 1 79 343.724 +71 2 79 5530.11 +71 3 79 3646.24 72 1 0 7 72 2 0 6 72 3 0 18 @@ -13030,6 +13243,9 @@ 72 9 59 0 72 10 59 0 72 11 59 0 +72 1 79 22.4242 +72 2 79 943.011 +72 3 79 215.571 73 1 0 8 73 2 0 4 73 3 0 17 @@ -13211,6 +13427,9 @@ 73 9 59 0 73 10 59 0 73 11 59 0 +73 1 79 5.66036 +73 2 79 1.61163 +73 3 79 54.0471 74 1 0 10 74 2 0 1 74 3 0 18 @@ -13392,6 +13611,9 @@ 74 9 59 0 74 10 59 0 74 11 59 0 +74 1 79 1830.1 +74 2 79 119.688 +74 3 79 17208.9 75 1 0 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b/test/scenarioGenotypes.xml index b9af6eab7..d24c464b5 100644 --- a/test/scenarioGenotypes.xml +++ b/test/scenarioGenotypes.xml @@ -32,6 +32,7 @@