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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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Extended CIGAR (sam v.1.4) #40

Closed aechchiki closed 7 years ago

aechchiki commented 7 years ago

Hi Ivan,

I wonder if there is a way to obtain an extended CIGAR string in the sam output by the current version of Graphmap, aka displaying detailed (X,=) for (match,mismatch) instead of M for alignment match (that can be match or mismatch).

Thanks in advance, Amina

isovic commented 7 years ago

Hi Amina! Sure, there is an option --extcigar that does this. Hope this helps, Best regards, Ivan.

aechchiki commented 7 years ago

Many thanks, that's exactly what I was looking for.

Cheers, Amina