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This repository was archived by the owner on Jul 29, 2025. It is now read-only.
This repository was archived by the owner on Jul 29, 2025. It is now read-only.

BUG: combining inline expansion and variable ref to .up or .down causes internal error #12

@daz10000

Description

@daz10000

Using a variable reference with a qualification for a subpart e.g. &locus.up inside a function which also uses inline sequences causes the internal error shown below. GSL internally creates GSL it can't process

E.g. this GSL

#refgenome S288C
#platform stitch
#linkers 0,2,3,9|
let func(locus)=
    &locus.up ; /$HI/ ; &locus.down
end
func(gYNG2)

emits this error with the compiler.

ParserError: near line 1 col 9
syntax error; found ';', expected one of ['>'].
=================================================================
#refgenome S288C
        ^
let func(locus)=
    &locus.up ; /$HI/ ; &locus.down
end

func(gYNG2)

InternalError: near line 3 col 5
An error occurred while parsing this internally-generated GSL source code:
gYNG2.up;/CACATC/ ;gYNG2.down
=================================================================
#refgenome S288C
let func(locus)=
    &locus.up ; /$HI/ ; &locus.down
    ^
end

func(gYNG2)

In contrast, this code

#refgenome S288C
#platform stitch
#linkers 0,2,3,9|
let func(locus)=
    &locus.up ; /$HI/ ; &locus.down
end

func(gYNG2)

compiles without issue. I think it's related to the order of expansion but I don't see why processing &locus.up later should make any difference.

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