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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

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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