Version 0.4.0

[timothymillar]

Features:

• Haplotype inclusion based on haplotype posterior threshold rather than genotype/phenotype #93
• Recalling genotypes based on observed haplotypes #93
• Removed per-sample filters and replaced with metadata for downstream filtering #96
• Options to call full genotype posterior or likelihoods over all genotypes #93
• Improve specification of per-locus assembly for better integration with asub #90
  • --region and --region-id arguments
  • --sample-bams argument
• Mechanism to cache log-likelihoods for reuse #21
• Enable caching of JIT compiled functions #94

Bug fixes:

• Fix bug in which read counts are ignored when excluding SNPs based on --mcmc-fix-homozygous threshold

VCF changes:

• Added fields:
  • INFO/DP
  • INFO/RCOUNT
  • INFO/NVAR
  • FORMAT/KMERCOV
  • FORMAT/MCI
  • FORMAT/GL
  • FORMAT/GP
• Removed fields:
  • FORMAT/DOSEXP