v1.0.0

Merge pull request #97 from kpalin/dev

Move AC INFO as AD FORMAT

v.0.4.5

• functionality to call tri-allelic SNVs (added by @ftostevin-ont)
• fix problem with outputting haplotagged bam file (also output index)

Version 0.4.4

v0.4.4

Version 0.4.4

Version 0.4.3

Minor fixes.

v0.4.2

• several bug fixes related to VCF specification
• minor changes to output files

v0.4.1

• Output single BAM. Add tags HP (haplotype) and PS (phase sets) to output reads.
• Work with CRAM files

v0.4.0

• added VCF input option for variants to genotype and phase
• changed default indel priors to enable indel calling with VCF

v0.3.5

fixed bug causing crash when chromosome has no variants

v0.3.4

Added filter flags to VCF output to avoid errors with BCFtools/other tools.

v0.3.3

• Fixed a bug causing values at the far left end of the alignment band not to be properly cleared out and then get re-used in subsequent dynamic programming iterations.