Merge pull request #248 from tcezard/relax_chrom_names

EVA-3586 - Allow colon in chromosome names
EBIvariation · Jul 2, 2024 · 76b0d2b · 76b0d2b
2 parents b1d7a46 + a426d63
commit 76b0d2b
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Showing 26 changed files with 4,304 additions and 3,224 deletions.
diff --git a/inc/vcf/error.hpp b/inc/vcf/error.hpp
@@ -225,7 +225,7 @@ namespace ebi
         using BodySectionError::BodySectionError;
         ChromosomeBodyError() : ChromosomeBodyError{0} {}
         ChromosomeBodyError(size_t line) : ChromosomeBodyError{line,
-            "Chromosome is not a string without colons or whitespaces, optionally wrapped with angle brackets (<>)"} { }
+            "Chromosome is not a string without whitespaces, optionally wrapped with angle brackets (<>)"} { }
         virtual ~ChromosomeBodyError() override { }
         virtual void apply_visitor(ErrorVisitor &visitor) override { visitor.visit(*this); }
     };

diff --git a/inc/vcf/file_structure.hpp b/inc/vcf/file_structure.hpp
@@ -330,19 +330,12 @@ namespace ebi
         void set_types();
 
         /**
-         * Checks that chromosome does not contain colons or white-spaces
+         * Checks that chromosome does not contain white-spaces
          *
          * @throw ChromosomeBodyError
          */
         void check_chromosome() const;
 
-        /**
-         * Checks that chromosome does not contain any colons
-         *
-         * @throw ChromosomeBodyError
-         */
-        void check_chromosome_no_colons() const;
-
         /**
          * Checks that chromosome does not contain any white-spaces
          *