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lh3 / gfa1

This repo is deprecated. Please use gfatools instead.
https://github.com/lh3/gfatools
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Negative overlap length #6

Closed ruanjue closed 6 years ago

ruanjue commented 6 years ago

Dear Heng,

I am trying to transform the clean assembly graph of WTDBG into GFA format. I wonder whether GFA support ngative overlap length in link. Simplely, can olen = -128? <overlap> ::= <olen> | <olen1>:<olen2> | <cigar>

Best, Jue

ruanjue commented 6 years ago

If olen can be negative, it will be easy for me to transform spare assembly graph.

lh3 commented 6 years ago

You can use negative length for now.

lh3 commented 6 years ago

For compatibility purpose (in particular with bandage), you would probably like to put the gap length in a tag like

L  A  +  B  +  0S  gl:i:100

Perhaps this is better.

ruanjue commented 6 years ago

Thanks!