Releases · sanger-tol/agp-tpf-utils

pretext-to-asm (renamed from pretext-to-tpf, but old alias retained) now handles FASTA input and output, removing dependencies on upstream and downstream scripts. Memory use is kept to a minimum using a 250 KB buffer, so genomes and chromosomes of any size can be processed.
Sorting and naming of chromosomes, which is also synced across haplotypes
Matching of haplotype tags to scaffold names is no longer case sensitive
Separate summary stats for each haplotype in a new <OUTFILE>.info.yaml file
New <OUTFILE>.chr_report.csv file shows Pretext scaffold name, sequence name and lengths for each chromosomal scaffold
New Target tag for when retained scaffolds are heavily outnumbered by Contaminant scaffolds to reduce tagging required
Unlocalised scaffolds can now be switched between haplotypes by adding the appropriate haplotype tag
Allow and correctly sort chromosomes with Roman numeral names (for nematodes)
New errors and warnings for:
- Unloc tags in un-painted scaffolds
- Location of single pixel gaps between cut scaffolds
- Error message if -a, --assembly and -p, --pretext arguments are switched
- Haplotig is tagged on a scaffold which is longer than the shortest chromosome
- The number of autosomes do not match across haplotypes

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