Add warning and correct urls

Clinical-Genomics · Nov 14, 2024 · d2dca53 · d2dca53
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Showing 3 changed files with 6 additions and 3 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -13,7 +13,7 @@ Try to use the following format:
 - The optional fields Source and Version are allowed in the VCF header([#106](https://github.com/Clinical-Genomics/genmod/pull/106))
 - Released the constraint on Python 3.8 (collections, pkg_resources to importlib, tests) ([#142](https://github.com/Clinical-Genomics/genmod/pull/142))
 - Update annotation examples ([#144](https://github.com/Clinical-Genomics/genmod/pull/144))
-
+- Updated documentation with warning about compounds only being scored within the first family in the VCF ([#151](https://github.com/Clinical-Genomics/genmod/pull/151)) 
 
 ## [3.9]
 - Fixed wrong models when chromosome X was named `chrX` and not `X` ([#135](https://github.com/Clinical-Genomics/genmod/pull/135))

diff --git a/docs/commands/build-annotation.md b/docs/commands/build-annotation.md
@@ -25,4 +25,4 @@ Options:
 ## Overview ##
 
 The build command is used for building new annotations. This could be used if another gene defenition than default (refSeq) are preferred, if other regions than genes should be used to annotate compounds or if another organism than humans are used in the analysis.
-The supported formats are `bed, ccds, gtf, gene_pred, gff`. Small examples for the supported formats in [conftest.py](https://github.com/moonso/genmod/blob/master/tests/conftest.py)
+The supported formats are `bed, ccds, gtf, gene_pred, gff`. Small examples for the supported formats in [conftest.py](https://github.com/Clinical-Genomics/genmod/blob/master/tests/conftest.py)
diff --git a/docs/commands/score-compounds.md b/docs/commands/score-compounds.md
@@ -2,6 +2,9 @@
 
 This module performs ranking of compound variants.
 
+> [!WARNING]
+> Ranking of compound variants is only done for the the first family in the VCF.
+
 During the ranking of these compounds the rank score might be modified in place.
 See `genmod/score_variants/compound_scorer.py:L248`.
 
@@ -17,4 +20,4 @@ or `(0, 1)` if it's of `RankScoreNormalized` type.
 
 In previous Genmod versions there were no such capping rule in effect.
 Earlier ranked variants from `compounds` module might show lower rank
-scores compared to this implementation.
+scores compared to this implementation.