merge of Petr's initial htslib completion
lots of changes
many edits including cleaned up interface for pbwtCursor and referencePhase().
referenceImpute() is unfinished/unfunctional as yet.
select and remove sites, referenceImpute and compareGenotypes (may be buggy), adding aFend to macs, vcf and gen parsing as now required by pbwtWrite
imputation off all best matches plus removeSites and a few bits
add .PHONY to makefile so make test actually runs the tests
add ability to write out VCF using htslib
add test for writeVcf
changes to let tests pass since addition of aFend. also readSites file was not storing variation correctly
free allocated memory to keep valgrind happy
Merge pull request #4 from sm15/feature/write_vcf

new -writeVcf option
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