Adding script for CNV's to master#17

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MaritIsKarel wants to merge 61 commits intomasterfrom

Commits on Sep 30, 2025

Copied SNV script for CNV data
Marit
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Unneccesary function removed.
Marit
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Define format for LUMC CNV file
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Process the LUMC CNV file.
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Safe data to the output file.
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Commits on Oct 8, 2025

Update the HGVS library to v0.5.5 to add support for PHP 7.4.
ifokkema
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Commits on Oct 17, 2025

Spelling and adding examples of lines found.
Marit
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Adding examples and removing comment.
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Removing enter.
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Adding examples and comment.
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Adding a break.
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If starting position is 1, change to pter.
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Reading Radboud file and checking for output file.
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Putting lines as comments.
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Commits on Oct 20, 2025

Get correct line to add to output file.
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Commits on Oct 31, 2025

Changing the heather for radboud.
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Changing 'size' to 'hgvs'.
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Adding comments.
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The changed version to check and validate the radboud data.
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Commits on Nov 3, 2025

Adding or correcting comments.
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Commits on Nov 4, 2025

Commits on Nov 6, 2025

Add basic version of the CNV processing file.
ifokkema
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Commits on Nov 13, 2025

Spelling.
Marit
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Adding comments and examples to explain what might needs to be changed.
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Expand explanation.
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Commits on Jan 13, 2026

Removing 'genes','gene' and 'published_as' because they are not needed for CNV's
Marit
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Removing unnecessary comments.
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Changing or adding comments.
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Replacing or removing variables that aren't used.
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Commits on Jan 14, 2026

Removing example of output which was used to see what that piece of code did.
Marit
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Correcting spelling.
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Comments we might need to discuss what to do with them.
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Removing unnecessary lines.
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Commits on Jan 16, 2026

Removing unnecessary comments that are cleared up.
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To check if the changes are correct. Not sure yet.
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Removing empty else loop.
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Adding back removed code that is still needed.
Marit
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Commits on Jan 19, 2026

Removing unnecessary code.
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Commits on Jan 20, 2026

Clarifying comments.
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Cleaning up the script.
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Removing unnecessary code.
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Without this line the data gets written to the database.
Marit
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Commits on Apr 16, 2026