v0.4.0

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.