genotypeCompare takes intersection of sites, fix compiler warning in hash.c, makefile_icc for optimised compilation with icc rather than gcc
Added -readHap command to read phased impute2/shapeit2 data
Change gen to hap in typeIO report
Merge pull request #5 from johnlees/master

jl11 changes to pbwt code - Richard checked with John
changes for new reference phasing, including cleaned up match extension
Merge branch 'master' of https://github.com/richarddurbin/pbwt

Merging back John Lees pull request changes into my changes for new reference phasing
advertise -writeVcf in the help message
keep track of situations where there are no overlaps during referenceImpute
Merge pull request #6 from sm15/feature/write_vcf_quickfix

advertise -writeVcf in the help message