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Feature/36725/birmingham status pathclass changes#106

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NImeson merged 7 commits into
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feature/36725/birmingham_status_pathclass_changes
Sep 24, 2024
Merged

Feature/36725/birmingham status pathclass changes#106
NImeson merged 7 commits into
developfrom
feature/36725/birmingham_status_pathclass_changes

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@NImeson

@NImeson NImeson commented Aug 16, 2024 •
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What?
During the CASREF QA , 34 records with incompatible teststatus and varpath class were identified for Birmingham (RQ3) -

33 records where teststatus is 1 and varpathclass is 3
1 record where teststatus is null and varpathclass is 3

Why?
For the 33 records, the importer was setting var path class 3 before duplicating the record for all genes in a panel, therefore the var path class gets duplicated along with it so even genes without a variant will be assigned path class 3 .

For the 1 record - this record was matching a "NO EVIDENCE' regex when there was additional information in there however there was also a note of a variant reclassification in there as well which was being filtered out

How?
Removed varpath assigning from the start of variant processing and now only assigning varpath class of 3 when a teststatus of 2 is assigned and IF 'UV' is present in the overall2 field.

Added an additional exception regex to the 'NO EVIDENCE' regex to account for this scenario

Testing?
Tests added to both BRCA and CRC handler test suites and variants counts performed and compared to those before changes were made.

mbis_development=# select * from restricted_variants where teststatus = 1 and variantpathclass = 3;
 pseudo_id1 | pseudo_id2 | codingdnasequencechange | gene | proteinimpact | servicereportidentifier | authoriseddate | variantpathclass | moleculartestingtype | genetictestscope | teststatus | exonintroncodonnumber | provider | sequencevarianttype | original_filename | raw_record | molecular_dataid 
------------+------------+-------------------------+------+---------------+-------------------------+----------------+------------------+----------------------+------------------+------------+-----------------------+----------+---------------------+-------------------+------------+------------------
(0 rows)

mbis_development=# select * from restricted_variants where teststatus is null and variantpathclass = 3;
 pseudo_id1 | pseudo_id2 | codingdnasequencechange | gene | proteinimpact | servicereportidentifier | authoriseddate | variantpathclass | moleculartestingtype | genetictestscope | teststatus | exonintroncodonnumber | provider | sequencevarianttype | original_filename | raw_record | molecular_dataid 
------------+------------+-------------------------+------+---------------+-------------------------+----------------+------------------+----------------------+------------------+------------+-----------------------+----------+---------------------+-------------------+------------+------------------
(0 rows)

@NImeson NImeson marked this pull request as ready for review September 23, 2024 14:42
shilpigoeldev
shilpigoeldev reviewed Sep 23, 2024
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@shilpigoeldev shilpigoeldev left a comment

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Changes make sense @NImeson thanks but have a think if the code can be DRYed up as can see repetitive code
@genocolorectal.add_status(2) @genocolorectal.add_variant_class(3) if @posnegtest == 'UV'.

@NImeson

NImeson commented Sep 24, 2024

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Changes make sense @NImeson thanks but have a think if the code can be DRYed up as can see repetitive code @genocolorectal.add_status(2) @genocolorectal.add_variant_class(3) if @posnegtest == 'UV'.

Refactored code into varpath method in latest commit :-)

@NImeson NImeson merged commit a0fe6ae into develop Sep 24, 2024
@NImeson NImeson deleted the feature/36725/birmingham_status_pathclass_changes branch September 24, 2024 11:34
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@NImeson @shilpigoeldev