add genotypeCompare text to help
added two lines to phase() to remove reverse PBWT which is not in fact the reverse of the final forwards one.  This also allows the resulting phased pbwt to be saved properly.
fix to cursor initialisation, new match algorithm, new reference phase method not great, perhaps more
added warn function
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
update for latest htslib API