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Vv ensembl dev susmi#660

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Peter-J-Freeman merged 86 commits intodevelopopenvar/variantValidator:developfrom vv_ensembl_dev_susmiopenvar/variantValidator:vv_ensembl_dev_susmiCopy head branch name to clipboardMar 5, 2025

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Commits on Dec 2, 2024

• Fixes that overcome NR transcripts with LOC based gene symbols in genes2transcripts functionality

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Commits on Dec 3, 2024

• Fixes the mapping of NC_000009.12:g.92474742delinsATCA back to NM_017680.6:c.153G>T in issue #651

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Commits on Dec 4, 2024

• Add tweaks to genes2transcripts to handle gene symbols that are updating and HGNC genes with no transcript info openvar/rest_variantValidator#186 and also handle the longer deletions in #651

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Commits on Dec 5, 2024

• Update the code to accept intronic variants in transcripts with alternate alignments in patches vs the primary assembly. Issue #657

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• code that deals with protein references with nucleotide variant types

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• Update position added for Ter=

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Commits on Dec 11, 2024

• Update vdb version and test issue 87

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Commits on Jan 9, 2025

• Changes to the code base to correct some unhandled descriptions e.g. 3 prime UTRs in uncertain positions for the LOVD paper

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Commits on Jan 14, 2025

• Expand code to handle expanded repeat syntax in allele descriptions

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Commits on Jan 16, 2025

• add in code to deal with common HGVS early stage typos like double colons

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Commits on Jan 17, 2025

• Additional code changes to handle failed variants reported by the LOVD team

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• Final commit before merge with parse bypass code

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Commits on Feb 10, 2025

• Reduce SeqRepo calls on hgvs to VCF mapping

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• Attempt to reduce SeqRepo calls when shifting

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Commits on Feb 17, 2025

• Don't re-build existing hgvs objects in mappers

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• Add a 'All' valid genomes flag to report_hgvs2vcf

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• Exploit new report_hgvs2vcf flag for output

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• Reduce unnecessary vcf re-generation from liftover

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• Use existing genomic vcf data in liftover

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• Add validation skip option, use in map fallback

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• Avoid parsing of hgvs from text hgvs_utils 1

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• Avoid parsing of hgvs from text hgvs_utils 2

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• Add hgvs object span handling to parts>delins func

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• Add object based equivalent to hgvs_dup2indel

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• Upgrade delins creation in gapped_mapping.py

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• Add a function to build new variants from existing

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Commits on Feb 26, 2025

• Improve hgvs obj handling for complex coordinates

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• Don't re-parse hgvs obj from strings MixinConv 1

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• Don't re-parse hgvs obj from strings MixinConv 2

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Commits on Mar 2, 2025

• Don't re-parse hgvs obj from strings MixinConv 3

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• Add extra test for chr_to_rsg

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• Allow obj for validateHGVS to avoid re-parse

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• Allow obj for genomic mapper to avoid re-parse

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• Return obj for chr_to_rsg to avoid re-parse

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• More re-parsing reductions for mappers.py

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• Reduce trivial re-parsing in vvMixinCore

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• Prevent re-parsing of relevant_transcripts output

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• Reduce re-parsing in vvMixinConverters.py

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• Do vcf style multi-alt variants without re-parsing

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• Further reduce re-parsing in format_converters.py

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• Remove last non-input re-parse in liftover

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• Improve ref-striping from hgvs obj

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• Variant.genomic_g str->hgvs obj, reduce re-parsing

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• Don't search for gene symbol on chr/transcript

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• Remove unneded re-parse from expanded_repeats

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• Reduce re-parsing in gapped_mapping.py

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• Remove final hgvs re-parsing from hgvs_utils.py

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• Don't unset ref for = type variants

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• Convert hgvs transcript variation to hgvs object

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• Test improved alt ref != selected genomic ref code

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• Remove last hgvs obj re-parses from vvMixinInit.py

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• Move hgvs obj conversion up a step in vvMixinCore

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• Move abort for con type variants before parsing

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• Return early and reduce indent on non c prot map

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• Exploit early return to reduce indent in prot map

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• Further use of returns to reduce indent in protmap

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• Add VVPosEdit for output formatting tweaks

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• Add helper functions for hgvs obj protein handling

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• Switch protein to use hgvs obj to avoid re-parsing

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• Add test for RNA indel -> prot del case

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Commits on Mar 3, 2025

• Move expanded repeat formatting before obj convert

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• Move input formatting before object creation point

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• Move methyl syntax suffix handling before obj conv

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• Update/improve tests for variant format_quibble

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• Reduce hgvs obj re-parsing in complex_descriptions

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• Slight output formatting improvement HGVS AA

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• Improve formatting hgvs output on prot/NA

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• Improve handling of bad mappings in gapped_mapping

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• Fix handling of ref type/source with obj not str

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• Make refseq mistake finder work for txt *and* obj

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• Harden initial convert to obj presence + parser

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• Handel t->c shift without declaring as a re-map

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• Harden against n variant issues in mapping

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• Add limited allele parser improvements

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• Fix use_checking to handle object quibble as well

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• Reduce unneeded exon fetch and re-start in mappers

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• Switch to early (singular) hgvs str->object parse

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• Add&use handing for checked variants resubmitted

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• Add methylation to VVPosEdit + PosEdit->VVPosEdit

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• Switch from text to VVPosEdit for methylation out

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Commits on Mar 4, 2025

• Merge pull request #663 from openvar/JFW_reparse_reduction

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• update tests where gene symbol HIF1A\-AS3 changed to HIF1A\-AS1

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Commits on Mar 5, 2025

• update tests where gene symbol HIF1A\-AS3 changed to HIF1A\-AS1

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• conflicting bug fix

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• Merge branch 'vv_ensembl_dev_susmi' of https://github.com/openvar/variantValidator into vv_ensembl_dev_susmi

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• final test edits for changes to the HIF1A-AS1 gene including the stable ids in testvariants 224 and 225

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