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EVA-3586 - Allow colon in chromosome names #248

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merged 10 commits into from
Jul 2, 2024
Merged

EVA-3586 - Allow colon in chromosome names #248

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e53a3b0
Allow colon in chromosome names
tcezard Jun 14, 2024
f2bc8b5
Add contig names that test presence of a colon
tcezard Jun 14, 2024
163b374
Regenerate the Ragel files update the C++ specific code
tcezard Jun 14, 2024
a75411c
fix comment
tcezard Jun 14, 2024
8de2a0e
Change unit test
tcezard Jun 14, 2024
512635a
Change unit test
tcezard Jun 14, 2024
42dee1f
Remove failed tests with colon
tcezard Jun 14, 2024
c6f5689
Revert long unsigned int to ::size_t
tcezard Jun 27, 2024
6838514
Revert spacing
tcezard Jun 27, 2024
a426d63
Apply suggestions from code review
tcezard Jun 27, 2024
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2 changes: 1 addition & 1 deletion inc/vcf/error.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -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); }
};
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9 changes: 1 addition & 8 deletions inc/vcf/file_structure.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -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
*
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