Feature/newcastle crc multivariant

[shilpigoeldev]

What?

In Newcastle CRC while scanning for multivariants , came across few genotypes that has mutation scanning more than one gene, these changes capture them.

Why?

Our importer must capture all variants with correct genes.

How?

By adding regex and methods to capture these identified genotypes.

Testing?

Relevant tests have been added and before and after counts have been checked as well.

[NImeson]

This is me being picky but please could we fix the gene name typo in the method name 'prepare_**grem1_**scg5_geno' ?

[shilpigoeldev]

Thanks @NImeson , committed in [20609a5]

[shilpigoeldev]

[like] GOEL, Shilpi (NHS ENGLAND - X26) reacted to your message:

________________________________ From: NImeson ***@***.***> Sent: Wednesday, February 12, 2025 2:03:40 PM To: NHSDigital/data_management_system ***@***.***> Cc: GOEL, Shilpi (NHS ENGLAND - X26) ***@***.***>; Author ***@***.***> Subject: Re: [NHSDigital/data_management_system] Feature/newcastle crc multivariant (PR #144) This message originated from outside of NHSmail. Please do not click links or open attachments unless you recognise the sender and know the content is safe. @NImeson commented on this pull request.

________________________________ In lib/import/colorectal/providers/newcastle/newcastle_handler_colorectal.rb<#144 (comment)>:

+ def process_variants(genocolorectals, genocolorectal, variant)

+ genes = variant&.scan(COLORECTAL_GENES_REGEX)&.flatten + + # For variant like "het dup GREM1 and SGC5" + if genes.present? && genes.all? { |gene| %w[GREM1 SCG5].include?(gene) } && variant.scan(/dup/i).size == 1 + prepare_germ1_scg5_genos(genocolorectals, genocolorectal, variant) + elsif genes.size > 1 + process_multi_genes(genocolorectals, genocolorectal, variant, genes) + else + process_mutations(genocolorectal, variant) + genocolorectals.append(genocolorectal) + end + genocolorectals + end + + def prepare_germ1_scg5_genos(genocolorectals, genocolorectal, variant) This is me being picky but please could we fix the gene name typo in the method 'prepare_**grem1_**scg5_geno' ? — Reply to this email directly, view it on GitHub<#144 (review)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ATZXVNURALJJRUO26I2YUQD2PNIDZAVCNFSM6AAAAABW7HZLTSVHI2DSMVQWIX3LMV43YUDVNRWFEZLROVSXG5CSMV3GSZLXHMZDMMJSGAZDMNRSG4>. You are receiving this because you authored the thread.Message ID: ***@***.***> ************************************************************************************** ****************************** This message may contain confidential information. If you are not the intended recipient please: i) inform the sender that you have received the message in error before deleting it; and ii) do not disclose, copy or distribute information in this e-mail or take any action in relation to its content (to do so is strictly prohibited and may be unlawful). Thank you for your co-operation. NHSmail is the secure email, collaboration and directory service available for all NHS staff in England. NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and other accredited email services. For more information and to find out how you can switch visit Joining NHSmail – NHSmail Support<https://support.nhs.net/article-categories/joining-nhsmail/>

[NImeson]

Looks good :-)