[LphyBeast] Missing integration test for unphase function

[kche309]

We are missing an integration test for testing the unphase function for Unphased data in LPhyBeast for GT16 and GT10.

• Requirements: The integration test needs to run the LPhyBeastCMD and using the LPhy model below and -seed=666 and make sure the same unphased genotype sequences are produced in the resulting XML.

• How this will help us? Adding this test will make managing changes to GT16 and GT10 easier. We only need to click rerun all Junit tests to check things are in working order.

Example LPhyBeast testing command (take note of paths in -vf)

lphybeast.LPhyBeastCMD -seed=666 -vf "phylonco-beast/version.xml,phylonco-lphybeast/version.xml,../flc/version.xml" -r 1 phylonco-lphy/examples/gt16CoalErrModelUnphase.lphy

Example LPhy model script

model {
  π ~ Dirichlet(conc=[3.0, 3.0, 3.0, 3.0, 3.0, 3.0, 3.0, 3.0, 3.0, 3.0, 3.0, 3.0, 3.0, 3.0, 3.0, 3.0]);
  rates ~ Dirichlet(conc=[1.0, 2.0, 1.0, 1.0, 2.0, 1.0]);
  Q = gt16(rates=rates, freq=π);
  Θ ~ LogNormal(meanlog=-2.0, sdlog=1.0);
  ψ ~ Coalescent(n=16, theta=Θ);
  A ~ PhyloCTMC(L=200, Q=Q, dataType=phasedGenotype(), tree=ψ);
  delta ~ Beta(alpha=1.5, beta=4.5);
  epsilon ~ Beta(alpha=2, beta=18);
  E ~ GT16ErrorModel(alignment=A, delta=delta, epsilon=epsilon);
  D = unphase(alignment=E);
}

Example LPhyBeast generated XML

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!--
model {
  π ~ Dirichlet(conc=[3.0, 3.0, 3.0, 3.0, 3.0, 3.0, 3.0, 3.0, 3.0, 3.0, 3.0, 3.0, 3.0, 3.0, 3.0, 3.0]);
  rates ~ Dirichlet(conc=[1.0, 2.0, 1.0, 1.0, 2.0, 1.0]);
  Q = gt16(rates=rates, freq=π);
  Θ ~ LogNormal(meanlog=-2.0, sdlog=1.0);
  ψ ~ Coalescent(n=16, theta=Θ);
  A ~ PhyloCTMC(L=200, Q=Q, dataType=phasedGenotype(), tree=ψ);
  delta ~ Beta(alpha=1.5, beta=4.5);
  epsilon ~ Beta(alpha=2, beta=18);
  E ~ GT16ErrorModel(alignment=A, delta=delta, epsilon=epsilon);
  D = unphase(alignment=E);
}

-->
<beast namespace="beast.core:beast.evolution.alignment:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.base.evolution.alignment:beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood" required="phylonco v1.2.1:phylonco v1.2.0" version="2.7">

    <data
id="D"
spec="Alignment"
dataType="nucleotideDiploid16">
        <sequence id="Sequence" spec="Sequence" taxon="0" totalcount="16" value="WYWMfYSffaa5faWMMKW55Ya5fMaKfafKWSY5YaYSYY5ffYW0RfMRR0KYffK5RYa5MRa0W5W5YaY005WK5MKWWaYa55Wa5ffKYRaM5RKWf5SM55KYfYS5WYfaaW5RYW0Yf5WR0aSWYKYaafRW0M5RMfW5aWKSSMY5afY5KfMRa0RK5WaM5K5MSKMS0aKK5WYa5RSY5Ya5"/>
        <sequence id="Sequence1" spec="Sequence" taxon="1" totalcount="16" value="WYWWKY5fRWa5fW555WfMSY5SWWYWfaYKYS55YaWafYMfYYRMaW5R0YRMW0W5WKRM0RR0fWK5Wa5M05MKMMaWYaaY55WaY0ffSfaM50Wfa5SMY5WKffS5WYfYRWYWKWMS55WfWRSffKSaaWWf0afMYff5aMKYYYYYKf55afMWafRW5aKY5W5MSKMSRKKf5R5SYMSY5YaW"/>
        <sequence id="Sequence2" spec="Sequence" taxon="2" totalcount="16" value="WYWWfYYRfKa5WaWMYfWMWYa5fWaKfR5KWaY5YaWKYK5WYY0WWfMR0Ma5WfKYRYaM50a0WYf5YaY5M5YY55KW0aKR55KR5ffKSfaM5K0WR5S0YSfYfYS5fffSaf5RfW0Yf50R0aSWYK5aSWaK0MfRWfR5fWaSSMY5aW55afMRSWRffWRM5K5MSaWS0aKf5R555RSS5Ya5"/>
        <sequence id="Sequence3" spec="Sequence" taxon="3" totalcount="16" value="WWfMfYSffKa5faWMMKW0MYa5fWaKfaYfWSY5YafSYY5WfY0WRf5Ra5K5WfK50KaWM0RMWYW5YaYMM5MK5MKWWafR55aa5ffKSRaM5RKWRMSMf5RffYa5WYfSKW5RfWW5f5W0WaSWYKYaaWRK00fR5fW5aWaSS5Y5aW55a0MRRfRK5fa55K5MSKMa0aKf5W5SMRSY5Ya5"/>
        <sequence id="Sequence4" spec="Sequence" taxon="4" totalcount="16" value="WYWMf5SKfKa5faWM0KW5MYaafMaKfaYKWSY55afSYY5ffYWWRf0RRMK5WfK5RfaW0Ra0KYW5YaYMM5MK5MfWfaKa55Wa5fffSRaM5RfWW5SMf5aYfSa5WYfaSW5RffWYf500faSWYKfaaWRW0MfRMfW5aWK5SMY5af55ffMRafMKYWa05K5MSaM50aKK5W5S5R555Ya5"/>
        <sequence id="Sequence5" spec="Sequence" taxon="5" totalcount="16" value="fYWWKfYfRWa5ffW5YWfMaYaSWW5ffaYKfSS5YaWMfYMfYaRMaf5RRMRMW0W5WYRMMaR0fYW5faaMM5MfMMRWYaaf55WaY0ffafa05WWf05SMfYWafYa5WYf5RfYWfWMSW5fYWRSffKSKaWWf0KYM5Yf5aKKSYMY5af55aW0WKWRW5aKY5W5MSKMSRaKf5R5SYRS555aW"/>
        <sequence id="Sequence6" spec="Sequence" taxon="6" totalcount="16" value="WYWWKf5fRWa5fWW5YWW5SYaSWWYWfaYKYSS5YaWSfY5f55RMaW5RRMRMW0W5WY0MMRR0f5W5WaSM55MKMMa0YaaW55WaYWWfKfa55W0fRSS5f5W5fYS50YfYRWYWfWMSW5WfWRSffKSfaWM50aYMYff5aMKSfMY5Kf55afMWKWMW5fKY5W5MSKM5RaKf5aSSYRSY5faW"/>
        <sequence id="Sequence7" spec="Sequence" taxon="7" totalcount="16" value="WYWWKf5fWWa5ffWSYWWSSYaSWWfffaYfYSS5YaKSfYMfY5RMaf5RRMa5R0W0WfR5MRR0fYW5WRSMM5MWM0aWYaaY05WafWWfSfaM5WWfRMSMY50Sf5S5WffYaWYWfMMYW5WWWMYYfKSfafff0KYM5ff5aMKYYMY5Kf55af5WKWRW5KKY5W5MSa5SRaKf5RSSYWSY5YaW"/>
        <sequence id="Sequence8" spec="Sequence" taxon="8" totalcount="16" value="WYW5K5SffKa5faW0MaRYMYaSfMaKWaYKfSY5YafS5Y5ffYWWRfMRRMK5WfK5RYaMMRa0WYW5YaYMM55K5MKWWaKa55fa5fffSRaM5RfWW55MY5KYfYS5WYfYaW5RfWWMf5WRfaafYK5aaWRK0MfRMfW5aWKSSMY5af55KfMRKWRKYWaM5KS0SaM50aKK5WYS5RSY5Ya5"/>
        <sequence id="Sequence9" spec="Sequence" taxon="9" totalcount="16" value="WYWWaf5fRWa5fWf5YWWMSYS5fW5ffaYKYSSMYaWSfYMfY5aMaW5RR5RMf0W5WYR5MRR0f5f5WaS5M5MKMMaWYaaY55WaY0WfSfaM50WfR5S5Y5W5fYS5WYfYRfYWfWMSW5WYWRSffKSKaWff0KYMYffSaMKYY5f5Kf55afMWKWRW5KaY5W5M5K5SRaKf5RSSYMSY5Ya0"/>
        <sequence id="Sequence10" spec="Sequence" taxon="10" totalcount="16" value="WYWWKf5f0Wa5ffWSYWWMSYaSWWYffa5aYSS5YaKSfY5fffRMaf5RRMa5R0W5ff05M0R0fYW5WaSMM5MfMWaWYaaYM5WaYWWf5fa55WWKR5SM55WSfYS5WWfYRWYWfM0SW5WWWMYfWK5KafKf0KYMYff5aMKYWMY5Kf5S5fMWKWRW5KK55W55Sf5SRaKf5R5S5RSW55aW"/>
        <sequence id="Sequence11" spec="Sequence" taxon="11" totalcount="16" value="WYWWfYYRfKK5faWMaYWMWYa5fWaafaYKWSY5YaWSYK5WYfWW0fMa05K5WfKYRY5M5Ra0WYaY5aY5M5YK55a0WaaR55K05ffYSfaM5RaRa5SMYSKYffS5WYfSKf5RfWWYf5fMWaSWYK5aaWRK0MfRWfW5KWaaaMf5aW55afMSfWRfYWR05K5MSKWS0aKf5RYS5RYS55a5"/>
        <sequence id="Sequence12" spec="Sequence" taxon="12" totalcount="16" value="WY0WKf5ffWa5fWWSMWRMMfaSWfYfKKYKYSS5YafSfYMfY5RMaY5aRMa5R0W5WfaMMRR0f5f5WaSMM5MWMMaWYaaY55WaK0YfSfaM5WffR5SMY5WSfKS5WYfYRWYff5MSW5WWW5SffKSaRfff0KYMYf05RMaSYMf5Kf55af0WKWRf5KKYYW5S5KMSRafW5RSS5aSY5YaW"/>
        <sequence id="Sequence13" spec="Sequence" taxon="13" totalcount="16" value="WYfMf5SffKa5faW0MaWMMYa0fWRKfaYKWa55YafMYYMffYWWafMaRMa5ffK5KYaMMRa0W5WYYa5MM5RK5MKWWaaR55Wa5fKKSaaM50KWR5SMY5KYfY55WYfSaf5RfYWYf5fRWaSWYK5aaWRK0MfRMfW5aWKSS0YSaW5MafMRWfRKYWaM5K5MSK5S0aff5WYY5RSY5Ya5"/>
        <sequence id="Sequence14" spec="Sequence" taxon="14" totalcount="16" value="0YWKfYYRffK5WaWMYfWMWYaSfWaKfW5KWSY5YaWSYfMWYYWWWfMR0MK5WffYRYaM5Ra0Wff5WaY5M5YK55KWWaKR5YKR5ffKSfaM5RK0R55MYSKYfYS5WYfSKf5Rf0WYfYWRWaSWYK5aafRf00fRWfW5aWaSSMY5aW55af5RKWafYWaM5K5MaaWa0aff5RYS5RSS5Ya5"/>
        <sequence id="Sequence15" spec="Sequence" taxon="15" totalcount="16" value="WYfMfYSffKK5faWMMa0M5YaSWWaKWaYKMM55YaWaY55ffYWW0fMRRMK5WfK5RYaM0aa0RYW5YaYMM5MK5SaWWaKR550a5ffKS0S55RKWR5aMY5fYfYS5WYfSaW5RfW0ff5WRWaSfYKYaaWRK0MfR5fW5RfKSS555aW55af0RaW0KYWa05a5MSK5S0aKf5WYS5RSY5Ya5"/>
    </data>

    <run id="MCMC" spec="MCMC" chainLength="1000000" preBurnin="400">
        <state id="State" spec="State">
            <parameter id="pi" spec="parameter.RealParameter" dimension="16" keys="0 1 2 3 4 5 6 7 8 9 a b c d e f" lower="0.0" name="stateNode" upper="1.0">0.01842714725596977 0.0602715339529201 0.0645674696761814 0.08443247925635905 0.044419527606908045 0.12569534841869384 0.023647744622917976 0.09112524622936682 0.04515749214782118 0.04796475530886209 0.09317052709067394 0.01740412970222331 0.09856003150979031 0.03819431876628042 0.04830520129469903 0.09865704716033259</parameter>
            <parameter id="rates" spec="parameter.RealParameter" dimension="6" keys="AC AG AT CG CT GT" lower="0.0" name="stateNode" upper="1.0">0.06942980118742885 0.29521252132645043 0.1741309599212491 0.07394439107697437 0.10367857677230066 0.2836037497155967</parameter>
            <parameter id="Theta" spec="parameter.RealParameter" lower="0.0" name="stateNode">0.14719887752321528</parameter>
            <stateNode id="psi" spec="beast.base.evolution.tree.TreeParser" IsLabelledNewick="true" newick="(((((15:0.034103863969536116,3:0.034103863969536116):0.010058513707970312,13:0.04416237767750643):0.014527600049709558,((4:0.0066406912473775575,0:0.0066406912473775575):0.002845532165884836,8:0.009486223413262393):0.049203754313953595):0.08199543010957833,(11:0.013656657604998564,(14:0.003734835366057427,2:0.003734835366057427):0.009921822238941138):0.12702875023179575):0.2594449289551014,((((9:5.431028616001842E-4,1:5.431028616001842E-4):0.026575599986929405,6:0.02711870284852959):0.0034323488909667153,5:0.030551051739496304):0.05086909208586862,(12:0.04007378879145088,(7:0.0033053558208531045,10:0.0033053558208531045):0.03676843297059778):0.041346355033914046):0.31871019296653075):0.0;">
                <taxonset id="TaxonSet" spec="TaxonSet">
                    <taxon id="0" spec="Taxon"/>
                    <taxon id="1" spec="Taxon"/>
                    <taxon id="2" spec="Taxon"/>
                    <taxon id="3" spec="Taxon"/>
                    <taxon id="4" spec="Taxon"/>
                    <taxon id="5" spec="Taxon"/>
                    <taxon id="6" spec="Taxon"/>
                    <taxon id="7" spec="Taxon"/>
                    <taxon id="8" spec="Taxon"/>
                    <taxon id="9" spec="Taxon"/>
                    <taxon id="10" spec="Taxon"/>
                    <taxon id="11" spec="Taxon"/>
                    <taxon id="12" spec="Taxon"/>
                    <taxon id="13" spec="Taxon"/>
                    <taxon id="14" spec="Taxon"/>
                    <taxon id="15" spec="Taxon"/>
                </taxonset>
            </stateNode>
            <parameter id="delta" spec="parameter.RealParameter" lower="0.0" name="stateNode" upper="1.0">0.1563852080878929</parameter>
            <parameter id="epsilon" spec="parameter.RealParameter" lower="0.0" name="stateNode" upper="1.0">0.05163510776823081</parameter>
        </state>
        <distribution id="posterior" spec="CompoundDistribution">
            <distribution id="prior" spec="CompoundDistribution">
                <distribution id="pi.prior" spec="distribution.Prior" x="@pi">
                    <distr id="Dirichlet" spec="distribution.Dirichlet">
                        <parameter id="RealParameter" spec="parameter.RealParameter" dimension="16" estimate="false" name="alpha">3.0 3.0 3.0 3.0 3.0 3.0 3.0 3.0 3.0 3.0 3.0 3.0 3.0 3.0 3.0 3.0</parameter>
                    </distr>
                </distribution>
                <distribution id="rates.prior" spec="distribution.Prior" x="@rates">
                    <distr id="Dirichlet1" spec="distribution.Dirichlet">
                        <parameter id="RealParameter1" spec="parameter.RealParameter" dimension="6" estimate="false" name="alpha">1.0 2.0 1.0 1.0 2.0 1.0</parameter>
                    </distr>
                </distribution>
                <distribution id="delta.prior" spec="distribution.Prior" x="@delta">
                    <distr id="Beta" spec="distribution.Beta">
                        <parameter id="RealParameter2" spec="parameter.RealParameter" name="alpha">1.5</parameter>
                        <parameter id="RealParameter3" spec="parameter.RealParameter" name="beta">4.5</parameter>
                    </distr>
                </distribution>
                <distribution id="Coalescent" spec="Coalescent">
                    <populationModel id="ConstantPopulation" spec="ConstantPopulation" popSize="@Theta"/>
                    <treeIntervals id="TreeIntervals" spec="beast.base.evolution.tree.TreeIntervals" tree="@psi"/>
                </distribution>
                <distribution id="Theta.prior" spec="distribution.Prior" x="@Theta">
                    <distr id="LogNormalDistributionModel" spec="distribution.LogNormalDistributionModel">
                        <parameter id="RealParameter4" spec="parameter.RealParameter" name="M">-2.0</parameter>
                        <parameter id="RealParameter5" spec="parameter.RealParameter" name="S">1.0</parameter>
                    </distr>
                </distribution>
                <distribution id="epsilon.prior" spec="distribution.Prior" x="@epsilon">
                    <distr id="Beta1" spec="distribution.Beta">
                        <parameter id="RealParameter6" spec="parameter.RealParameter" name="alpha">2.0</parameter>
                        <parameter id="RealParameter7" spec="parameter.RealParameter" name="beta">18.0</parameter>
                    </distr>
                </distribution>
            </distribution>
            <distribution id="likelihood" spec="CompoundDistribution">
                <distribution id="D.treeLikelihood" spec="phylonco.beast.evolution.likelihood.TreeLikelihoodWithErrorFast" implementation="beast.base.evolution.likelihood.TreeLikelihood" tree="@psi" useAmbiguities="true" useTipLikelihoods="true">
                    <errorModel id="GT16ErrorModel" spec="phylonco.beast.evolution.errormodel.GT16ErrorModel" delta="@delta" epsilon="@epsilon">
                        <datatype id="NucleotideDiploid16" spec="phylonco.beast.evolution.datatype.NucleotideDiploid16"/>
                    </errorModel>
                    <data idref="D"/>
                    <siteModel id="SiteModel" spec="SiteModel">
                        <substModel id="GT16" spec="phylonco.beast.evolution.substitutionmodel.GT16" nucRates="@rates">
                            <frequencies id="Frequencies" spec="Frequencies" frequencies="@pi"/>
                        </substModel>
                    </siteModel>
                    <branchRateModel id="StrictClockModel" spec="beast.base.evolution.branchratemodel.StrictClockModel">
                        <parameter id="RealParameter8" spec="parameter.RealParameter" name="clock.rate">1.0</parameter>
                    </branchRateModel>
                </distribution>
            </distribution>
        </distribution>
        <operator id="Theta.scale" spec="kernel.BactrianScaleOperator" parameter="@Theta" upper="10.0" weight="1.0"/>
        <operator id="delta.scale" spec="kernel.BactrianScaleOperator" parameter="@delta" upper="10.0" weight="1.0"/>
        <operator id="deltaExchangePair1" spec="operator.DeltaExchangeOperator" delta="0.0625" weight="1.0">
            <parameter idref="pi"/>
            <weightvector id="IntegerParameter" spec="parameter.IntegerParameter" dimension="16" lower="0" upper="0">0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0</weightvector>
        </operator>
        <operator id="deltaExchangePair2" spec="operator.DeltaExchangeOperator" delta="0.0625" weight="1.0">
            <parameter idref="pi"/>
            <weightvector id="IntegerParameter1" spec="parameter.IntegerParameter" dimension="16" lower="0" upper="0">0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0</weightvector>
        </operator>
        <operator id="deltaExchangePair3" spec="operator.DeltaExchangeOperator" delta="0.0625" weight="1.0">
            <parameter idref="pi"/>
            <weightvector id="IntegerParameter2" spec="parameter.IntegerParameter" dimension="16" lower="0" upper="0">0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0</weightvector>
        </operator>
        <operator id="deltaExchangePair4" spec="operator.DeltaExchangeOperator" delta="0.0625" weight="1.0">
            <parameter idref="pi"/>
            <weightvector id="IntegerParameter3" spec="parameter.IntegerParameter" dimension="16" lower="0" upper="0">0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0</weightvector>
        </operator>
        <operator id="deltaExchangePair5" spec="operator.DeltaExchangeOperator" delta="0.0625" weight="1.0">
            <parameter idref="pi"/>
            <weightvector id="IntegerParameter4" spec="parameter.IntegerParameter" dimension="16" lower="0" upper="0">0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0</weightvector>
        </operator>
        <operator id="deltaExchangePair6" spec="operator.DeltaExchangeOperator" delta="0.0625" weight="1.0">
            <parameter idref="pi"/>
            <weightvector id="IntegerParameter5" spec="parameter.IntegerParameter" dimension="16" lower="0" upper="0">0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0</weightvector>
        </operator>
        <operator id="epsilon.scale" spec="kernel.BactrianScaleOperator" parameter="@epsilon" upper="10.0" weight="1.0"/>
        <operator id="pi.deltaExchange" spec="operator.DeltaExchangeOperator" weight="6.656775051475124">
            <parameter idref="pi"/>
        </operator>
        <operator id="psi.BICEPSEpochAll" spec="EpochFlexOperator" fromOldestTipOnly="false" scaleFactor="0.1" tree="@psi" weight="1.624504792712471"/>
        <operator id="psi.BICEPSEpochTop" spec="EpochFlexOperator" scaleFactor="0.1" tree="@psi" weight="1.0"/>
        <operator id="psi.BICEPSTreeFlex" spec="TreeStretchOperator" scaleFactor="0.01" tree="@psi" weight="6.656775051475124"/>
        <operator id="psi.narrowExchange" spec="Exchange" tree="@psi" weight="6.656775051475124"/>
        <operator id="psi.rootAgeScale" spec="kernel.BactrianScaleOperator" rootOnly="true" tree="@psi" upper="0.975" weight="1.0"/>
        <operator id="psi.subtreeSlide" spec="kernel.BactrianSubtreeSlide" size="0.04001303367918957" tree="@psi" weight="6.656775051475124"/>
        <operator id="psi.uniform" spec="kernel.BactrianNodeOperator" tree="@psi" weight="6.656775051475124"/>
        <operator id="psi.wideExchange" spec="Exchange" isNarrow="false" tree="@psi" weight="1.7187719275874789"/>
        <operator id="psi.wilsonBalding" spec="WilsonBalding" tree="@psi" weight="1.7187719275874789"/>
        <operator id="rates.deltaExchange" spec="operator.DeltaExchangeOperator" weight="3.0851693136000478">
            <parameter idref="rates"/>
        </operator>
        <operator id="swapPair1" spec="operator.SwapOperator" parameter="@pi" weight="0.5">
            <filter id="BooleanParameter" spec="parameter.BooleanParameter" dimension="16">false true false false true false false false false false false false false false false false</filter>
        </operator>
        <operator id="swapPair2" spec="operator.SwapOperator" parameter="@pi" weight="0.5">
            <filter id="BooleanParameter1" spec="parameter.BooleanParameter" dimension="16">false false true false false false false false true false false false false false false false</filter>
        </operator>
        <operator id="swapPair3" spec="operator.SwapOperator" parameter="@pi" weight="0.5">
            <filter id="BooleanParameter2" spec="parameter.BooleanParameter" dimension="16">false false false true false false false false false false false false true false false false</filter>
        </operator>
        <operator id="swapPair4" spec="operator.SwapOperator" parameter="@pi" weight="0.5">
            <filter id="BooleanParameter3" spec="parameter.BooleanParameter" dimension="16">false false false false false false true false false true false false false false false false</filter>
        </operator>
        <operator id="swapPair5" spec="operator.SwapOperator" parameter="@pi" weight="0.5">
            <filter id="BooleanParameter4" spec="parameter.BooleanParameter" dimension="16">false false false false false false false true false false false false false true false false</filter>
        </operator>
        <operator id="swapPair6" spec="operator.SwapOperator" parameter="@pi" weight="0.5">
            <filter id="BooleanParameter5" spec="parameter.BooleanParameter" dimension="16">false false false false false false false false false false false true false false true false</filter>
        </operator>
        <logger id="ScreenLogger" spec="Logger" logEvery="50000">
            <log idref="posterior"/>
            <log idref="likelihood"/>
            <log idref="prior"/>
            <log idref="pi"/>
            <log idref="rates"/>
            <log idref="Theta"/>
            <log idref="delta"/>
            <log idref="epsilon"/>
        </logger>
        <logger id="Logger" spec="Logger" fileName="gt16CoalErrModelUnphase.log" logEvery="500">
            <log idref="posterior"/>
            <log idref="likelihood"/>
            <log idref="prior"/>
            <log idref="pi"/>
            <log idref="rates"/>
            <log idref="Theta"/>
            <log idref="delta"/>
            <log idref="epsilon"/>
            <log id="TreeStatLogger" spec="beast.base.evolution.tree.TreeStatLogger" tree="@psi"/>
            <log idref="D.treeLikelihood"/>
        </logger>
        <logger id="psi.treeLogger" spec="Logger" fileName="gt16CoalErrModelUnphase.trees" logEvery="500" mode="tree">
            <log idref="psi"/>
        </logger>
    </run>

</beast>

[yaox1818]

I used LPhyBeastCMD and -seed 666 to run the lphy script and got this xml file. The value of all parameters are same with the example.
gt16CoalErrModelUnphase.xml

[kche309]

Thanks for checking Yao. My idea is to have it automated so you don't have to rerun it manually to recheck each time.
Similar to this example https://github.com/CompEvol/beast2/blob/master/test/test/beast/integration/XMLProducerTest.java

But instead of testing parsing XMLs, we test that LPhyBeastCMD produces the XML with the same data by calling LPhyBeastCMD in the code. You'll also want to store the expected output in the test directory (in this case the full XML or the alignment data produced from the XML).