v1.1.5-dev

Fixed bug in SatmutUtilsToDiMSum. WT count not previously estimated accurately.

v1.1.3-dev-multi

Fixed bug in SatmutUtilsToDiMSum. WT count not previously estimated accurately.

v1.1.4-dev

Fixed bug in HGVS annotations for out-of-frame duplications > 1 nt.

v1.1.3-dev

Ensure HGVS annotations use uppercase bases to ensure compatibility with MAVEdb.

Fixed run_mave_hgvs_annot.py script to require target BED and fix bug in deletion-insertion MAVE-HGVS string.

v1.1.1-dev-multi

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.

Added a script (run_mave_hgvs_annot.py) for post-processing *summary.txt files to adjust HGVS positions relative to target regions as opposed to a coding sequence.

Ensure HGVS annotations use uppercase bases to ensure compatibility with MAVEdb.

Fixed description of the call algorithm in the manual.

v.1.1.2-dev

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. Added a script for post-processing *summary.txt files to adjust HGVS positions relative to target regions as opposed to a coding sequence.

v1.1.1-dev

Fixed unintended reversion to 1.1.0-dev-multi logic for MNP calling.

v1.1.0-dev

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

v1.1.0-dev-multi

Added support for simple insertion and deletion calling. Added MAVE-HGVS annotations. v1.1.0-dev-multi differs from v1.1.0-dev by enabling multivariant calling for more than two codon changes.

v1.0.4-dev

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.