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CHANGELOG.md

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UDF-BioUtils Changelog

v1.4.0 (2024-10-28)

  • Added function sort_site_list for numerically sorting a string of comma-separated integers, as returned by group_concat()'s.
  • INTERNAL: Removed redundant inline function split_by_substr_view and instead used the already-existing split_by_substr function.

v1.3.1 (2024-10-16)

  • Optimized functions sort_alleles and sort_list_unique for efficiency.
  • Updated documentation

v1.3 (2024-10-04)

  • Added distance function tn_93 for calculating Tamura-Nei (TN-93) Distance between two aligned nucleotide sequences, with optional parameter for gamma correction for variability of mutations among sites.

v1.2 (2024-08-22)

  • Added aggregate functions alphanumeric_entropy, nt_entropy, aa_entropy, and codon_entropy which will calculate the Shannon information entropy for alphanumeric strings, nucleotides, amino acids and codons respectively (the latter three expect only one per record).
  • Added scalar function alnum_entropy to calculate the Shannon entropy of an alphanumeric string.

v1.1 (2024-07-27)

  • Changed the annotation for glycosylation in mutation_list_gly and mutation_list_indel_gly from reporting -ADD-GLY and -LOSS-GLY to the more conventionally accepted (CHO+), (CHO+/-), and (CHO-).
  • mutation_list_gly and mutation_list_indel_gly will ignore . (which represents an unresolved base at the 3` or 5` end) in a sequence but will correctly treat - as a gap.
  • Unit tests are changed to test for whether . is correctly ignored in mutation_list_gly and mutation_list_indel_gly.