Support oncoanalyser v2 #6
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Pull Request Overview
This PR updates the SV prioritization logic to support oncoanalyser v2 by adjusting the read support fields and input tags.
- Updated the header fields in the SV TSV output to include VF_alt, SB_alt, and SF_alt.
- Modified the selection of read support fields to use the SVTYPE tag instead of EVENTTYPE.
- Enhanced error handling in parse_read_support_field with explicit error messaging and process termination.
Comments suppressed due to low confidence (1)
bolt/workflows/sv_somatic/prioritise.py:99
- [nitpick] Consider renaming 'eventtype' to 'sv_type' to more clearly reflect that it corresponds to the 'SVTYPE' field, improving overall code clarity.
eventtype = record.INFO.get('SVTYPE', '')
scwatts
requested changes
May 12, 2025
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Pending question in umccr/gpgr#88 (review) re switching to strand bias (SB) rather than DF / SF
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Uptade sv prioritize to take eSVee input with specific tags