- 10 Feb, 2022 10 commits
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Fokkema authored
Fixed various notices throughout LOVD
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Fokkema authored
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Fokkema authored
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Fokkema authored
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Fokkema authored
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Fokkema authored
We used to do quick checks on $_AUTH['level'], but $_AUTH can also be false. This now triggers notices in newer PHP versions. Replacing all calls to fix these notices. Starting with the ajax scripts.
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Fokkema authored
Improve `lovd_getVariantInfo()` and `lovd_fixHGVS()`
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Fokkema authored
Removed some unneded code, resorted two tests, re-added one test.
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Fokkema authored
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Fokkema authored
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- 09 Feb, 2022 7 commits
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Fokkema authored
Positions in the 3' UTR weren't handled well yet.
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Fokkema authored
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Fokkema authored
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Fokkema authored
Added tests for lovd_fixHGVS() that were recently added for lovd_getVariantInfo().
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Fokkema authored
The first is extracted and processed; then the type is overwritten by ";" and an ENOTSUPPORTED is added. Possible warnings that can occur from correct HGVS descriptions of combined variants are removed. This suffices for now.
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Fokkema authored
These now throw an ENOTSUPPORTED as long as they don't match the regex; otherwise they already threw a WSUFFIXGIVEN. We currently don't prevent this as that's for a later step when we decide to properly support them. At least like this, we'll get positions and we can recognize them and therefore allow these variants to be entered in LOVD.
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Fokkema authored
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- 08 Feb, 2022 4 commits
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Fokkema authored
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Fokkema authored
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Fokkema authored
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Fokkema authored
These are variants taken straight from VCF fields, like g.100A>AT that should be g.100_101insT, or even more complex variants like g.100ATGA>AA that should be g.101_102del. Empty ALTs are supported, so g.100A>. becomes g.100del. However, empty REFs are not supported as it's unclear where the insertion should take place. Either way, an empty ALT is not a valid VCF file.
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- 07 Feb, 2022 4 commits
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Fokkema authored
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Fokkema authored
... based on a start position (given in the format of lovd_getVariantInfo()) and a variant length (1 being the minimum).
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Fokkema authored
These are constructed from VCF files and are translated into substitutions. The NN>N or N>NN types we already recognize. Now also recognize variants where either the REF or the ALT was left empty, like N>. or even .>N - both of which are actually bugs in the VCF file generator.
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Fokkema authored
g.?_(?_?)insAAAA can still be fixed.
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- 03 Feb, 2022 7 commits
- 02 Feb, 2022 1 commit
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Fokkema authored
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- 01 Feb, 2022 4 commits
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Fokkema authored
This is now a bit simplistic; the main regex is now case-insensitive, the prefix is forced to be lowercase, and the variant type is forced lowercase unless for substitutions, WT variants, and repeats - those are forced into uppercase. For bsrC an exception is made. The suffix is left as is and is not checked.
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Fokkema authored
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Fokkema authored
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Fokkema authored
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- 31 Jan, 2022 3 commits
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Fokkema authored
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Fokkema authored
Now separately checking full positions passed with refseqs.
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Fokkema authored
It was running regexes over the whole suffix, which sometimes led to infinite recursion. Now, the suffix is split and all parts are checked. This fixes the infinite recursion and will also allow us to check suffixes better.
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