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ae4ba92
Copied SNV script for CNV data
Sep 30, 2025
813a45b
Unneccesary function removed.
Sep 30, 2025
aa1d1bb
Define format for LUMC CNV file
Sep 30, 2025
27e301e
Process the LUMC CNV file.
Sep 30, 2025
f4d9998
Safe data to the output file.
Sep 30, 2025
30c5f47
Add the LOVD/HGVS library as a submodule.
ifokkema Oct 1, 2025
3d571c4
Update the README; clarify how to activate the LOVD HGVS submodule.
ifokkema Oct 1, 2025
f23e4a2
Load the LOVD HGVS library in the CNV formatter.
ifokkema Oct 1, 2025
f87e7ec
Actually load the LOVD HGVS library.
ifokkema Oct 1, 2025
3691f29
Update the HGVS library to v0.5.5 to add support for PHP 7.4.
ifokkema Oct 8, 2025
b77023b
Spelling and adding examples of lines found.
Oct 17, 2025
69e39bf
Adding examples and removing comment.
Oct 17, 2025
2578508
Removing enter.
Oct 17, 2025
a0bc12b
Adding examples and comment.
Oct 17, 2025
81ead07
Adding a break.
Oct 17, 2025
478c7ae
If starting position is 1, change to pter.
Oct 17, 2025
03b1989
Reading Radboud file and checking for output file.
Oct 17, 2025
e76ee83
Putting lines as comments.
Oct 17, 2025
a6d2cc8
Get correct line to add to output file.
Oct 20, 2025
2ddd500
Changing the heather for radboud.
Oct 31, 2025
bfe6527
Changing 'size' to 'hgvs'.
Oct 31, 2025
a5250e6
Adding comments.
Oct 31, 2025
5273b82
The changed version to check and validate the radboud data.
Oct 31, 2025
95f34c8
Adding or correcting comments.
Nov 3, 2025
f2b02ab
Writing explanation for test data.
Nov 4, 2025
41f9326
Removing unnecessary lines (with example lines).
Nov 4, 2025
dbe8b9c
Explanation for the examples per situation.
Nov 4, 2025
c8bdd9e
Make the file executable, clean input file names, whitespace fixes.
ifokkema Nov 4, 2025
53d2f37
Renamed a few columns in the Radboud file.
ifokkema Nov 4, 2025
61c0c81
Simplify some code a bit.
ifokkema Nov 4, 2025
870de2b
Fix PHP notice thrown when parsing newer data.
ifokkema Nov 4, 2025
747477e
Update all syndrome names to their official terms.
ifokkema Nov 4, 2025
77e09da
Rename g.pter_qterdup to g.pter_qtersup.
ifokkema Nov 4, 2025
2422551
Detect qter from given positions for all chromosomes.
ifokkema Nov 4, 2025
0ea02b1
Simplify the code.
ifokkema Nov 4, 2025
db70dac
Add basic version of the CNV processing file.
ifokkema Nov 6, 2025
7169585
Spelling.
Nov 13, 2025
197b67b
Adding comments and examples to explain what might needs to be changed.
Nov 13, 2025
78cbcaa
Expand explanation.
Nov 13, 2025
ecd73ce
Removing 'genes','gene' and 'published_as' because they are not neede…
Jan 13, 2026
c66d063
Removing unnecessary comments.
Jan 13, 2026
ef64694
Changing or adding comments.
Jan 13, 2026
4cb4fcf
Replacing or removing variables that aren't used.
Jan 13, 2026
cec495e
Removing example of output which was used to see what that piece of c…
Jan 14, 2026
0eb36b5
Correcting spelling.
Jan 14, 2026
6737ace
Comments we might need to discuss what to do with them.
Jan 14, 2026
6a50cb7
Removing unnecessary lines.
Jan 14, 2026
bcb62b2
Removing unnecessary comments that are cleared up.
Jan 16, 2026
75ddde8
To check if the changes are correct. Not sure yet.
Jan 16, 2026
0ac34ee
Removing empty else loop.
Jan 16, 2026
ab97c12
Adding back removed code that is still needed.
Jan 16, 2026
55461e2
Removing unnecessary code.
Jan 19, 2026
4263e20
Clarifying comments.
Jan 20, 2026
5e9a125
Cleaning up the script.
Jan 20, 2026
ba9e822
Removing unnecessary code.
Jan 20, 2026
a8a0ed8
Without this line the data gets written to the database.
Jan 20, 2026
c679dc6
reformatting the layout of the position checking process for the Radb…
Apr 16, 2026
1428ce1
Spelling correction.
Apr 16, 2026
8c616c2
Reformatting from if loops to an array for the classifications.
Apr 16, 2026
18759b2
Reversing spelling changes to the correct version.
Apr 16, 2026
a833095
Putting back the lines of code in case debugging is needed.
Apr 16, 2026
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3 changes: 3 additions & 0 deletions .gitmodules
Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
[submodule "libs/HGVS-syntax-checker"]
path = libs/HGVS-syntax-checker
url = git@github.com:LOVDnl/HGVS-syntax-checker.git
10 changes: 10 additions & 0 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,16 @@ This script will take their export files, normalize and map the variants,
If previous records are found, they will be updated.
Records no longer found in LOVD3 will only be marked as removed, if the user requests so.

### Installation

This repository include a "submodule" of the LOVD HGVS library.
After downloading this repository, you'll need to activate this submodule separately in order to use it.
Run the following code in the terminal to activate submodules and to download the LOVD HGVS library.

```bash
git submodule init && git submodule update
```

### Grouping the center's raw data files

We used to work with the grouped file generated by the Groningen center.
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