update for latest htslib API
update example to use -readMacs instead of -macs
Merge pull request #10 from arq5x/master

update example to use -readMacs instead of -macs
Merge pull request #8 from sm15/master

update for latest htslib API
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
change hack in paint() to divide p->M by 5, not fix at 20
readVcfGT: split non-biallelic records rather then skipping

- Split non-biallelic records into biallelic records.

	```
	T	A,C	0|0	0|1	1|0	1|1	1|2	0|2	2|0	2|1	2|2
	```

	becomes

	```
	T	A	0|0	0|1	1|0	1|1	1|0	0|0	0|0	0|1	0|0
	T	C	0|0	0|0	0|0	0|0	0|1	0|1	1|0	1|0	1|1
	```

- add test for reading an writing a VCF
- treat haploid genotypes in the non-PAR region as diploid A/A
- convert tabs to spaces
add timeUpdate() to die()
change the way sample names are managed
explore phasing options
initial likelihood functions
add pbwtLikelihood.c
Merge pull request #12 from mcshane/feature/non-biallelic

readVcfGT: split non-biallelic records rather then skipping
add refFreq to Site structure and fill in when imputating
add imputeInfo to Site
change die feedback in unpack3
bug fix; was writing sentinel to yMissing not xMissing - remove yMissing (no longer needed)
switch to IDEA3 as default