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fix: do not report deleted or duplicated reference in hgvs.c notation #199

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fix: do not report deleted or duplicated reference in hgvs.c notation #199

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32c5ad9
fix: do not report deleted or duplicated reference in hgvs.c notation
tedil Jul 31, 2024
ed9617d
adjust tests to follow hgvs recommendations
tedil Jul 31, 2024
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8 changes: 4 additions & 4 deletions src/parser/display.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -86,10 +86,10 @@ impl Display for NaEdit {
(_, 0) => write!(f, "del{count}ins"),
(_, _) => write!(f, "del{count}ins{alternative}"),
},
NaEdit::DelRef { reference } => write!(f, "del{reference}"),
NaEdit::DelRef { .. } => write!(f, "del"),
NaEdit::DelNum { count } => write!(f, "del{count}"),
NaEdit::Ins { alternative } => write!(f, "ins{alternative}"),
NaEdit::Dup { reference } => write!(f, "dup{reference}"),
NaEdit::Dup { .. } => write!(f, "dup"),
NaEdit::InvRef { reference } => write!(f, "inv{reference}"),
NaEdit::InvNum { count } => write!(f, "inv{count}"),
}
Expand Down Expand Up @@ -782,7 +782,7 @@ mod test {
reference: "T".to_string()
}
),
"delT".to_string()
"del".to_string()
);
}

Expand Down Expand Up @@ -816,7 +816,7 @@ mod test {
reference: "T".to_string()
}
),
"dupT".to_string()
"dup".to_string()
);
}

Expand Down
12 changes: 6 additions & 6 deletions tests/data/parser/gauntlet
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Original file line number Diff line number Diff line change
Expand Up @@ -48,9 +48,9 @@ AC_01234.5:g.1_22A>T
#!unsupported: AC_01234.5:g.123_124[4]
#!unsupported: AC_01234.5:g.123_678conNG_012232.1:g.9456_10011
AC_01234.5:g.5dup
AC_01234.5:g.5dupT
AC_01234.5:g.5dup
AC_01234.5:g.7_8dup
AC_01234.5:g.7_8dup
AC_01234.5:g.7_8dupTG


# complex -- same allele (maybe)
Expand Down Expand Up @@ -88,9 +88,9 @@ AC_01234.5:c.76A>C
AC_01234.5:c.76_77delinsTT
AC_01234.5:c.76_77insT
AC_01234.5:c.76_78del
AC_01234.5:c.76_78delACT
AC_01234.5:c.76_78del
AC_01234.5:c.77_79dup
AC_01234.5:c.77_79dup
AC_01234.5:c.77_79dupCTG
AC_01234.5:c.88+1G>T
AC_01234.5:c.89-2A>C

Expand All @@ -100,9 +100,9 @@ AC_01234.5:c.89-2A>C
#!unsupported: AC_01234.5:g.123_124[4]
#!unsupported: AC_01234.5:g.123_678conNG_012232.1:g.9456_10011
AC_01234.5:g.5dup
AC_01234.5:g.5dupT
AC_01234.5:g.5dup
AC_01234.5:g.7_8dup
AC_01234.5:g.7_8dup
AC_01234.5:g.7_8dupTG



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