check_ped() to return corrected pedigree data in the result list instead of assigning objects to the global environmentmadc2vcf_all integration tests on CRAN while keeping them enabled in GitHub Actionsdosage2vcf now validates marker and sample sets between report and counts files, then aligns counts to the report order before writing VCF genotypesCHROM and POS are derived from Chrom/ChromPos when present, otherwise from MarkerName; MarkerName is retained in the VCF ID field-/NA) are written as diploid missing genotypes (./.)madc2vcf_multi to convert a DArTag MADC file to a VCF using the polyRAD pipeline for multiallelic genotypingcheck_madc_sanity before loading the data and stops with informative errors if:
RefAltSeqs = FALSE)FixAlleleIDs = FALSE)Chr_Pos format and no markers_info is providedmarkers_info: optional path or URL to a CSV with CloneID/BI_markerID, Chr, and Pos columns; required when CloneIDs do not follow the Chr_Pos formatcheck_botloci to validate and reconcile CloneIDs between the MADC and botloci file, automatically fixing padding mismatchesreadDArTag only when needed (all-NA rows/columns detected, CloneIDs remapped by check_botloci, or botloci IDs remapped)madc_file, botloci_file, and markers_infopolyRAD::TestOverdispersion, iterates priors with polyRAD::IterateHWE, and exports the result with polyRAD::RADdata2VCFpolyRAD is a soft dependency (listed under Suggests); an informative error is raised if it is not installedOther alleles:
add_others: if TRUE (default), alleles labeled "Other" in the MADC are included in off-target SNP extractionothers_max_snps: discards Other alleles with more than this many SNP differences relative to the Ref sequence (default: 5)others_rm_with_indels: discards Other alleles containing insertions or deletions relative to the Ref sequence (default: TRUE)merge_countsDetails:
both functions targets and all (targets + off-targets) markers now have check_madc_sanity function implemented. It tests:
Better messages if verbose = TRUE in madc2vcf_all
madc2vcf_all support for Indels - markers_info with Indels position is required; only the target indel is extracted, off-targets are ignored for the tag
madc2vcf_targets doesn’t run if:
madc2vcf_all in case they want to extract them as wellSee the table for madc2vcf_targets requirements accordingly to MADC content:
| check status | get_REF_ALT | Requires -- | -- | -- | -- IUPAC | TRUE | TRUE | markers_info REF/ALT | TRUE | FALSE | - | FALSE | TRUE | botloci or markers_info REF/ALT | FALSE | FALSE | - Indels | TRUE | TRUE | markers_info REF/ALT | TRUE | FALSE | - | FALSE | TRUE | botloci or markers_info REF/ALT | FALSE | FALSE | - ChromPos | TRUE | TRUE | botloci or markers_info REF/ALT | TRUE | FALSE | - | FALSE | TRUE | markers_info CHR/POS/REF/ALT or markers_info CHR/POS/ + botloci | FALSE | FALSE | markers_info CHR/POS FixAlleleIDs | TRUE | TRUE | botloci or markers_info REF/ALT | TRUE | FALSE | - | FALSE | TRUE | markers_info REF/ALT | FALSE | FALSE | -
vmsg to organize messages printed on the consolemadc_object to get_countsMADC to avoid reading the MADC file twice and to get directly the MADC fixed padding output from check_botlocimadc2vcf_targets checkscollapse_matches_counts and verbose to madc2vcf_targets functioncheck_madc_sanity. Currently, it checks for the presence of required columns, whether fixed allele IDs were assigned, the presence of IUPAC codes, lowercase sequence bases, indels, and chromosome and position information.markers_info, which allows users to provide a CSV file with marker information such as CHROM, POS, marker type, and position of indels. For BI species, this information is available from PanelHub.madc2vcf_all.DESCRIPTION.