v0.7.2

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 (./.)

What's Changed

• Madc2vcf updates by @Cristianetaniguti in #53
• Madc2vcf and Pedigree functions updates by @Cristianetaniguti in #54
• Dosage2vcf update by @alex-sandercock in #60
• CRAN 7.2 submission by @alex-sandercock in #61

Full Changelog: v0.6.2...v0.7.2

v0.6.2

What's Changed

• Added new functions thinSNP() and madc2gmat()
• Bug fixes for the madc2vcf_target() and madc2vcf_all() functions

v0.5.5

This PR focuses on function updates, documentation improvements, and bug fixes in preparation for the CRAN submission. Key changes include improved messaging in functions (using message() in place of cat()), enhanced error handling (especially in functions recovering reference/alternative alleles), and updates to documentation and examples.

• Updated function documentation and examples across several R scripts.
• Replaced cat() calls with message() for consistency in user feedback.
• Refactored error handling in functions such as add_ref_alt and check_ped.
• Updated the madc2vcf() function to madc2vcf_targets, and changed get_OffTargets() to madc2vcf_all()

v0.4.2

• Minor update to the check_ped() function

v0.4.1

Minor bug fixes

v0.4.0

New functions and bug fixes:

• get_offTargets: obtain the target and off-target SNPs from a fixedAllele MADC file
• madc2vcf: obtain the read count information for target SNPs only from a fixedAllele MADC file and convert to VCF format

v0.3.4

• Bug fixes

Bug fix v0.3.1

Fixed a bug with the filterVCF function where values in the INFO column were causing errors.

v0.3.0

• Updated documentation
• Updated citation information
• Added filter.VCF function to filter VCF files or vcfR objects

v0.2.0

Two functions have been added for this release:

• The clean_pedigree function was changed to the check_ped function.
  • The function now alerts the user to the errors present within the pedigree and provides the sample IDs in conflict.
• The dosage2vcf function was added
  • This function produces a VCF file from the DArT Dose Report and DArT Counts file.