Madc2vcf and Pedigree functions updates

[Cristianetaniguti]

Updates on madc2vcf functions

Details:

• If verbose = TRUE, the functions output informative messages along the process
• 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
• 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:

	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	-

• madc2vcf_targets got a new argument: collapse_matches_counts, if TRUE, it collapses the read counts of the RefMatch to Ref and AltMatch to Alt. Default is FALSE.

• madc2vcf_all have three new arguments: add_others, others_max_snps, others_rm_with_indels

• Users now have the option to generate multiallelic VCF - new function madc2vcf_multi

• madc2vcf_all doesn’t run if:

  • MADC Column names are not correct
  • If it is raw MADC
  • If it has IUPAC codes

• See the table for madc2vcf_all requirements accordingly to MADC content:

	Check status	Requires
Indels	TRUE	markers_info REF/ALT/IndelPos/IndelLenght + botloci
	FALSE	botloci
ChromPos	TRUE	botloci
	FALSE	markers_info CHR/POS + botloci
RefAltSeqs	TRUE	botloci
	FALSE	botloci + microhapdb

• madc2vcf_multi doesn’t run if:

• • MADC Column names are not correct
  • If it is raw MADC
  • If it has IUPAC codes
  • if there are absent Ref or Alt tags

• See the table for madc2vcf_all requirements accordingly to MADC content:

	Check status	Requires
Indels	TRUE	botloci
	FALSE	botloci
ChromPos	TRUE	botloci
	FALSE	markers_info CHR/POS + botloci

• test scripts were added and simulated MADC files were created to test all scenarios in all madc2vcf functions. Test files are located at: https://github.com/Breeding-Insight/BIGapp-PanelHub/tree/long_seq/test_madcs
• updated version, packages Imports in DESCRIPTION and functions documentations