Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

Unreleased

Added

Add command line option --hp_min_fix_length to fix homopolymers of at least the given length, so that they match the reference sequence.

Fixed

Do not run bcftools norm when using global align, because it could result in inconsistency between VCF and output sequences
Fix bug in global alignment, where alignment was forced to end at the end of the query sequence. Instead, allow it to stop earlier otherwise had some strange alignments that were incorrect (ending with a long gap and then a single aligned base, instead of aligned base, then a long gap)
Make indel calling consistent by putting gaps in consistent places.

0.4.0

Added

Added new command line option --global_align to both command line tasks vcf_eval and make_truth_vcf. This is meant for small (eg covid) genomes, where both truth and reference are one sequence only. It is less efficient but more accurate.
Added command line options that only apply when --global_align is used: --global_align_min_coord, --global_align_max_coord, --sanitise_truth_gaps, --use_non_acgt,
If using --global_align, writes an MSA of rev and truth sequences, and a FASTA of the truth sequence, but with santised gap lengths.
New tag in VCF file VCF_QRY_VARIANT, which is the variant with respect to the query sequence, as opposed to the ref sequence.

Fixed

various edge cases caught when there are indels and/or Ns in sequences
edge case caused by indels when making VCF with --global align.