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lh3 / gfa1

This repo is deprecated. Please use gfatools instead.
https://github.com/lh3/gfatools
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Bug in bubble popping algorithm #7

Open snurk opened 4 years ago

snurk commented 4 years ago

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.

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snurk commented 4 years ago

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 commented 4 years ago

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.