Satmut-utils

Added support for simple insertion and deletion calling. Added MAVE-HGVS annotations.

Added support for simple insertion and deletion calling. Added MAVE-HGVS annotations.

Fixed bug where relative file paths for the output directory caused the alignment workflow to fail.

Fixed bug where relative file paths caused the alignment workflow to fail. Removed the filtering of GFF records that annotate contigs with RefSeq accession identifiers (NT or NW), as filtering may lead to errors with custom reference files specifying a contig that begins with NT or NW.

Fixed bug where relative file paths for the FASTQs caused the alignment workflow to fail. Removed the filtering of GFF records that annotate contigs with RefSeq accession identifiers (NT or NW), as filtering may lead to errors with custom reference files specifying a contig that begins with NT or NW.

Moved run_design_conversion.py from prototype to scripts directory