v0.2-release

Major changes and improvements:

• When reads in VCF files, it can exclude sites from list which were specified in a file, flags -vcf and -exclude now can work together.
• Reorganised the testing data, and example data.
• Include tools (written in R) to explore and interpret data and output.
• Improved documentation

Bug fixed:

• Typo in unittest

v0.2-beta

Major changes and improvements:

• Program, repo names changed to DEploid
• Support for reading in VCF, and output in VCF
• Print out posterior probabilities at the final iteration, which allows us to do "painting" to the reference panel
• Record starting and end times
• Support debug temp files to record position when recomb or miscopying occur

Bug fixed:

• position output should be an integer rather than a double
• when updating haplotypes, the probability index was wrong

v0.1-beta

Major changes and improvements:

• allow copying from the same strain during update pair of haplotypes at the same time ( default )
• added flags to include const recomb prob and miss copy prob
• added flags to exclude sites
• update haplotypes moves are accomplished by chromosomes
• added utilities for assessing results
• update unittests

Bug fixed:

• index off when copying path from the panel

v0.1-alpha: Merge pull request #28 from mcveanlab/debugUpdatePair

make a tag before optimization