cleanup
Adding sbt build system
Adding sbt build system
clean up file closing code
Bug fixes for Ref storage, trying mutable Buffers
Signficantly simplify PhaseBlock travesal
Mostly working some oddities with Phase, increasing Phase cutoff and adding support for unphased indviduals
Mostly working some oddities with Phase, increasing Phase cutoff and adding support for unphased indviduals
Phase now reports nearest block if not in block\nSeveral Logic errors in Phase fixed\nRemoved Chr reporting for Ref
correction to permutation test to catch both forward and reverse Genotypes ie 0/1 & 1/0
Disable use of Nearest phaseblock
Fixes to Phasing and Parent GT check
various fixes
premerge