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maickrau / GraphAligner

MIT License
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Removal of --global-alignment #39

Open briannadon opened 3 years ago

briannadon commented 3 years ago

I noticed that a few days ago, --global-alignment was removed. Our group was using this as a way to ensure appropriate alignment of the short reads we're using, being aware that this tool is meant for long reads. We would also like to use --global-alignment in conjunction with the hidden --multiseed-DP 1 option to inspect equivalent alignment handling in a global and local alignment context.

What was the reason for the removal of --global-alignment, and can it be restored, or was that due to a bug or undesired behavior?

maickrau commented 3 years ago

It was removed to simplify the code. I didn't know anyone used --global-alignment. For now you can use eg. commit 5217838 which has both --global-alignment and --multiseed-DP

RolandFaure commented 2 years ago

Hello, We'd like to force long alignments on our graph. That is because we're working on a genome full of repeats and we want to force the long reads to bridge the repeats. The --global-alignment option was really useful for that. Do you have an alternative set of parameters we could use ? Thanks in advance

Euphrasiologist commented 2 years ago

I have quite noisy, low quality but very long reads to align. I thought the --global-alignment option would be good for this. Do you recommend this? Or any other parameters?

Thanks!