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This repository has been archived by the owner on Nov 2, 2019. It is now read-only.

Bug in bubble popping algorithm #7

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snurk opened this issue Oct 25, 2019 · 2 comments
Open

Bug in bubble popping algorithm #7

snurk opened this issue Oct 25, 2019 · 2 comments

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@snurk
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snurk commented Oct 25, 2019

I believe there is a bug in bubble popping algorithm that leads to a removal of bubbles with (seemingly arbitrary long) tips of any orientation. See attached gfa (called my.txt to trick github attach dialogue).
my.txt
Despite looking like this in Bandage it is being simplified into a single unambiguous path by the -b option of gfaview.
image

@snurk
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snurk commented Oct 25, 2019

BTW, while trying to extract a smaller example with the -s option I ran into an issue that gfaview -s list.txt -S 3 was still giving me a set of (3) disconnected nodes.
list.txt

@lh3
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lh3 commented Nov 2, 2019

I will mark this repo deprecated as most of the gfaview functionalities are supported by the asm command of gfatools. You can create an issue at gfatools instead.

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