Changelog

0.2.0 (unreleased)

New functions

  • simGL.ref_alt_to_index() — converts reference and alternate allele strings to ACGT integer indices, for use with simGL.subset_GL().

  • simGL.GL_to_vcf() — writes a VCF 4.2 file from normalized biallelic GLs and allele read counts, with GT, GL, and AD FORMAT fields.

Bug fixes

  • simGL.incorporate_monomorphic(): fixed incorrect indexing when start > 0. The output array is sized end - start but absolute genomic positions were previously used as array indices.

  • simGL.subset_GL(): fixed an IndexError when all allele pairs were already in ascending order (the empty index array defaulted to float64 and could not be used as an integer index).

Improvements

  • simGL.allelereadcounts_to_GL(): the error rate e must now be strictly greater than zero. A new validator raises TypeError for e = 0 with an informative message referencing the ANGSD default.

  • Extended docstrings for all public functions, including parameter descriptions, return types, and usage notes.

  • Fixed spelling errors (dimetion → dimension, inputed → inputted, beggining → beginning) throughout the source code.

0.1.0

Initial release.