polyrad_bugfix

[Cristianetaniguti]

• Bugfix polyRAD dosage call

  • DosageCall_functions.R:
    • fix names match between Geno and hindhe.obj
    • genotypes from polyrad now named GTP in VCF format - to avoid redundancy with GT if VCF already has genotype called
  • mod_DosageCall.R
    • polyrad_items$vcf_path was replaced by polyRAD_dosage_call result
  • Add test
    • example file iris_DArT_VCF.vcf.gz didn’t have chromosome IDs in the header

• Bugfix on vcf_sanity_check

  • Avoid first five columns (Marker ID included) to check for | (phased genotypes)

[alex-sandercock]

Will need to revisit this at a later point to overwrite the existing GT info with the polyRAD info, but this works for now.