vamos-v3.0.4

This release fixes an off-by-1 error in sequences that are extracted.

A change in behavior is introduced as well that considers the tandem repeat sequence as starting at the base after the last non-TR base and ending one before the first non-TR base after the locus. This will include insertions that are mapped to the beginning or end of a locus, which is consistent with left-aligning of indels.

The consensus module was changed from abPOA to spoa.

The following options are added:
-Z Treat input as zero-based, half-open coordinates.
-E Print the reconstructed TR sequence based on the motif decomposition in the vcf genotype field.
-l Use local alignment to potentially trim start/end from annotations.