BIGr 0.7.2

• Fixed manual text errors

BIGr 0.7.1

• Updated check_ped() to return corrected pedigree data in the result list instead of assigning objects to the global environment
• Skipped long remote madc2vcf_all integration tests on CRAN while keeping them enabled in GitHub Actions

BIGr 0.7.0

Updates on dosage2vcf

• Added support for DArT SNP/INDEL 1-row and 2-row report formats
• dosage2vcf now validates marker and sample sets between report and counts files, then aligns counts to the report order before writing VCF genotypes
• VCF CHROM and POS are derived from Chrom/ChromPos when present, otherwise from MarkerName; MarkerName is retained in the VCF ID field
• Missing SNP/INDEL genotype calls (-/NA) are written as diploid missing genotypes (./.)

New function madc2vcf_multi

• New function madc2vcf_multi to convert a DArTag MADC file to a VCF using the polyRAD pipeline for multiallelic genotyping
• Runs check_madc_sanity before loading the data and stops with informative errors if:
  • Required columns are missing
  • IUPAC (non-ATCG) codes are present in AlleleSequence
  • Ref/Alt sequences are unpaired (RefAltSeqs = FALSE)
  • Allele IDs have not been fixed by HapApp (FixAlleleIDs = FALSE)
  • CloneIDs do not follow Chr_Pos format and no markers_info is provided
• New argument markers_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 format
• Runs check_botloci to validate and reconcile CloneIDs between the MADC and botloci file, automatically fixing padding mismatches
• A corrected temp file is written and passed to readDArTag only when needed (all-NA rows/columns detected, CloneIDs remapped by check_botloci, or botloci IDs remapped)
• Accepts paths or URLs for madc_file, botloci_file, and markers_info
• Estimates overdispersion with polyRAD::TestOverdispersion, iterates priors with polyRAD::IterateHWE, and exports the result with polyRAD::RADdata2VCF
• polyRAD is a soft dependency (listed under Suggests); an informative error is raised if it is not installed

BIGr 0.6.6

Updates on madc2vcf_all

• New arguments for controlling processing of Other alleles:
  • add_others: if TRUE (default), alleles labeled “Other” in the MADC are included in off-target SNP extraction
  • others_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)
• Others alleles that carry a different base at the target SNP position are now reported as a 3rd allele in the VCF instead of being silently dropped
• Target position is now correctly removed from Others alignments, preventing duplicate VCF positions and marker IDs
• Fixed a bug where Others alleles with “Ref_” or “Alt_” in their AlleleID would corrupt the target SNP REF/ALT fields and read depth counts in merge_counts
• Improved verbose messages throughout: counts of Other alleles found, kept, and discarded (by indel filter and by max SNP filter) are now reported; multiallelic target SNPs with a 3rd allele from Others are counted and reported
• Debug-level message (level 3) listing each Other allele added and its genomic position

BIGr 0.6.5

Updates on madc2vcf functions

Details:

• both functions targets and all (targets + off-targets) markers now have check_madc_sanity function implemented. It tests:
  • [Columns] If MADC has the expected columns
  • [allNArow | allNAcol] Presence of columns and rows with all NA (happens often when people open the MADC in excel before loading in R)
  • [IUPACcodes] Presence of IUPAC codes on AlleleSequence
  • [LowerCase] Presence of lower case bases on AlleleSequence
  • [Indels] Presence of Indels
  • [ChromPos] If CloneID follows the format Chr_Pos
  • [RefAltSeqs] If all Ref Allele has corresponding Alt and vice-versa
  • [OtherAlleles] If “Other” exists in the MADC AlleleID
• 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:
  • MADC Column names are not correct
  • Ignore Other alleles - but inform the user if they exist or not and direct them to madc2vcf_all in case they want to extract them as well
• See the table for madc2vcf_targets requirements accordingly to MADC content:

BIGr 0.6.4

• Add function vmsg to organize messages printed on the console
• Add metadata to VCF header from madc2vcf_targets
• Add argument madc_object to get_countsMADC to avoid reading the MADC file twice and to get directly the MADC fixed padding output from check_botloci
• Organize messages from madc2vcf_targets checks
• Add argument collapse_matches_counts and verbose to madc2vcf_targets function

BIGr 0.6.3

• New function to check MADC files: check_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.
• Added new argument 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.
• Checked inputs for madc2vcf_all.
• Updated affiliation in DESCRIPTION.

BIGr 0.6.2

• Fixed the doi and name list in the CITATION file

BIGr 0.6.1

• Added new functions for filtering MADC files and converting to relationship matrices
• Added function thinSNPs to thin SNPs based on physical distance
• Added bug fixes and improvements to existing functions

BIGr 0.5.5

• Updated DESCRIPTION
• Added return value for merge_MADCs
• Added optional seed for check_ped
• Added verbose option

BIGr 0.5.4

• Updated dosage2vcf example

BIGr 0.5.3

• Updated madc2vcf_all example

BIGr 0.5.2

• madc2vcf function changed to madc2vcf_targets
• get_OffTargets function changed to madc2vcf_all
• Updates to testthat tests and function examples

BIGr 0.5.1

• Improvements of testthat tests
• Add check_replicates and check_homozygous_trios for pedigree relationship quality check

BIGr 0.5.0

• Add imputation_concordance function to estimate accuracy of imputed and original dataset
• Add get_OffTargets function to extract target and off-target SNPs from a MADC file
• Add merge_MADCs function to merge two or more MADC files together
• Improved documentation and examples for all functions
• Add tests for all functions

BIGr 0.3.3

• Adapt updog2vcf to model f1, f1pp, s1 and s1pp

BIGr 0.3.2

• updog2vcf function option to output compressed VCF (.vcf.gz) - set as default
• remove need for defining ploidy
• add metadata at the VCF header