Add per genotype vaccine efficacy

[acavelan]

Add the possibility to specify per genotype vaccine efficacy for all the three vaccines implemented in OpenMalaria:

• PEV
• TBV
• BSV

The VACCINE_GENOTYPE model option must be set.

When the VACCINE_GENOTYPE option is set, the user MUST provide a phenotype description including initialEfficay values for each locus and allele defined in the parasiteGenetics section of the xml.

...
<PEV> <!--assuming csp (from RTS.S-A01), anti-circumsporozoit -->
        <decay L="7.32" k="0.69" function="weibull"/>
        <efficacyB value="10.0"/>   <!-- efficacyB is used in beta distribution to assign efficacy of vaccine to an individual, allows heterogeneity-->
        <phenotype name="sensitive">
                <restriction onLocus="x" toAllele="sensitive"/>
                <initialEfficacy value="0.91"/>
                <initialEfficacy value="0.49"/>
        </phenotype>
        <phenotype name="resistant">
                <restriction onLocus="x" toAllele="resistant"/>
                <initialEfficacy value="0.91"/>
                <initialEfficacy value="0.49"/>
        </phenotype>
</PEV>
...
<parasiteGenetics samplingMode="tracking">
        <!-- Define name/freq/fitness of the locus/alleles defined in the drugPD code -->
        <locus name="x">
                <allele fitness="1" initialFrequency="0.5" name="sensitive"/>
                <allele fitness="1" initialFrequency="0.5" name="resistant"/>
        </locus>
</parasiteGenetics>
...

When VACCINE_GENOTYPE is set, nExpected is no longer affected by the PEV vaccine. Only the reporting is affected, and the simulation will work as expected.

When VACCINE_GENOTYPE is NOT set, then the above will work as usual for consistency with older versions.