add strand flip check

[alkaZeltser]

This PR adds allele match checking and strand flip correction functionality.

For some background on strand flipping, check out my new discussion post:
#68

@RoniHaas I would appreciate your review of the key strand flip function (assess.pgs.vcf.allele.match)

Closes #63

• Add DNA flip function (flips alleles to reverse complement)
• Add allele match check function (checks for various mismatch cases including strand flip, and corrects strand flips)
• Incorporate strand flip checking into the main apply.polygenic.score function
• Add tests for above
• Update all documentation (README, manual, vignette)
• Export all relevant new functions through NAMESPACE
• Update NEWS with new feature

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Testing Results

All unit tests pass

[alkaZeltser]

For those who are interested, check out the rendered manual:
ApplyPolygenicScore_2.0.0.pdf

And the rendered User Guide vignette:
UserGuide.pdf

[dan-knight]

These boolean flag arguments are a good opportunity to add clarity and establish default functionality. Just adding TRUE or FALSE defaults might go a long way here to implying the primary use case(s).

EDIT: Nevermind. Seems like you do that on the higher-level function. That's ideal. Sorry!!

[rachelmadang]

LGTM!

[RoniHaas]

Looks good, I think all possible cases have been addressed!

[alkaZeltser]

Thanks everyone! @forbiddenpersimmon @dan-knight next PR will be coming soon, and it's gonna be a release PR for new version and checks for next CRAN submission