how to get the supplementary alignment

isovic / graphmap

GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:

https://github.com/lbcb-sci/graphmap2

MIT License

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how to get the supplementary alignment #105

Open WellJoea opened 3 years ago

WellJoea commented 3 years ago

I used graphmap with the command as follows:

$GRAPHMAP align \ 
    -r $REF \ 
    -i $IDX \ 
    -d $FQ \ 
    -t 20 \ 
    --ambiguity 0.02 \ 
    --secondary \ 
  -o $OU

But, the result cannot get the secondary and supplementary alignment.