Feature/35183/oxford handler#56
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shilpigoeldev
requested changes
Jan 30, 2024
| def convert_nil_to_zero(count) | ||
| count = 0 if count.nil? | ||
| count | ||
| end |
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This method is not needed.
| geneticscope = record.raw_fields['scope / limitations of test'] | ||
| geneticscope.scan(/panel|scree(n|m)|brca|hcs|panel/i).size.positive? | ||
| geneticscope.scan(/panel|full\s?screen|full\sscreem|full\sgene\sscreen| | ||
| brca_multiplicom|hcs|brca1|brca2|CNV.*only|CNV.*analysis| |
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Can it be moved to constants please, similarly targeted check too?
shilpigoeldev
requested changes
Jan 30, 2024
| \s?(?<variant>del|inv|dup)/ix | ||
| EXON_REGEX = /(?<mutationtype>del|inv|dup).+ion\s(?:of\s)?exons?\s?(?<exons>[0-9]+(?:-[0-9]+)?)| | ||
| ex(?:on|ons)?\s?(?<exons>[0-9]+(?:(?:-|\+)[0-9]+)?)\s?(?<mutationtype>del|inv|dup)| | ||
| (?<mutationtype>del|inv|dup).+ion\sBRCA1\sexons?\s(?<exons>[0-9]+-(?:[0-9]*))| |
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Can it be made more generic ex- [a-z ]+ rather BRCA1 to be able to extract mutation and exonic location irrespective of what comes ex- BRCA2 rather BRCA1?
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@shilpigoeldev- the variant counts are the same after the changes for both brca and colorectal |
shilpigoeldev
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Jan 31, 2024
shilpigoeldev
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shilpigoeldev
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Thanks @lauramccluskey1 ..looks good to me.. Happy to approve if the counts are matching and QAed by Fiona.
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Details on this change can be found on ticket 35183 and include:
Variant counts have been checked as part of QA process.