Merge branch 'master' of https://github.com/sm15/pbwt

also add some non-final changes to referencePhase3 in pbwtImpute.c
new pbwtPaint.c with paint command for chromopainter like coancestry matrix building
changes to referencePhase; still not good enough
refactoring of cursor ADU operations into AD operations and U calculation - much cleaner
new readPhase command to read Li and Stephens PHASE style files - transposed so can be memory hungry
bug fix in fgetword() in utils.c (I think!) needed for readPhase()
refactoring of match within commands in pbwtMatch.c to facilitate paint
Merge branch 'master' of https://github.com/richarddurbin/pbwt

rddurbin/pbwt