CHANGES.txt

Release Summary:

1.0.0, April 15, 2022
	Initial release of satmut_utils

1.0.0+001, April 18, 2022
	Added minimum versions for dependencies. Download satmut_utils from pip during creation of conda environment.

1.0.1, November 21, 2022
	Fixed bug where default --nthreads argument causes variant calling to fail during consensus deduplication.

1.0.2, December 9, 2022
	Fixed variant calling bug that caused di-nt MNPs to be called as two SNPs when the di-nt MNP was downstream of a single SNP or another di-nt MNP.

1.0.3, June 23, 2023
	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.
	
1.0.4, June 27, 2023
	Fixed bug where relative file paths for the output directory caused the alignment workflow to fail.
	
1.1.0, September 11, 2023
	Added support for simple insertion and deletion calling. Added MAVE-HGVS annotations.
	
1.1.1, September 15, 2023
	Fixed bugs in HGVS annotations for single in-frame insertions and MNPs spanning the CDS-3' UTR junction. Ensure deletion-insertion annotations follow HGVS proposal SVD-WG010.
	
1.1.2, December 25, 2023
	Fixed bug in HGVS annotations for out-of-frame duplications > 1 nt.