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@timothymillar timothymillar released this 18 May 03:53
· 275 commits to master since this release
v0.4.0
c46b94c
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Learn about vigilant mode.

New 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
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