Packages 
Package Description
Correlation
Provides classes for calculating LD using different methods.
Exceptions
Provides various exceptions
Executable
Provides the LinkImpute main class
Files
Provides class for dealing with data files.
Files.VCFData
Provides classes for dealing with VCF files.
Files.VCFMappers
Provides classes that help convert string vcf data to other data types.
Mask
Provides classes for masking genotypes for testing imputation accuracy.
Methods
Provides the actual imputation classes.
Similarity
Provides classes for calculating similarity (based on LD) between SNPs.
Utils
Provides various utility classes.