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CHANGES.txt
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CHANGES.txt
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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-dev, November 21, 2022
Fixed bug that caused satmut_utils 'call' to fail when running consensus deduplication with --nthreads 0
Added additional pre- and post-processing scripts for conversion between satmut_utils and DiMSum, dms_tools2, and Enrich2 data formats
1.0.1-dev001, November 21, 2022
Added back modeling_utils.r to prototype directory
1.0.1-dev002, November 28, 2022
Fixed links to point to ijhoskins repo in installation script
Fixed links to manual in README.md to point to ijhoskins
1.0.2-dev, 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-dev, December 19, 2022
Added back run_design_conversion.py to prototype directory
Added __init__.py to prototype directory. Now in package.
Fixed URL links in setup.cfg and in satmut_utils_manual.md to point to ijhoskins repo
1.0.3-dev001, January 2, 2023
Moved run_design_conversion.py from prototype to scripts directory
1.0.4-dev, July 3, 2023
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.
1.1.0-dev, September 11, 2023
Added support for simple insertion and deletion calling. Added MAVE-HGVS annotations.
1.1.1-dev, September 11, 2023
Fixed unintended reversion to 1.1.0-dev-multi logic for MNP calling.
1.1.2-dev, 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. Added a script for post-processing *summary.txt files to adjust HGVS positions relative to target regions as opposed to a coding sequence.
1.1.3-dev, November 14, 2023
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.
1.1.4-dev, December 25, 2023
Fixed bug in HGVS annotations for out-of-frame duplications > 1 nt.
1.1.5-dev, May 31, 2024
Fixed bug SatmutUtilsToDiMSum. WT count not previously estimated accurately.