printing duplicate (I think) lines

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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printing duplicate (I think) lines #41

Open jwasmuth opened 7 years ago

jwasmuth commented 7 years ago

Hi, I'm using graphmap (0.3.1) align with the -Z option and occasionally have duplicated alignment printed twice. I've attached the reference, example reads and the output in sam format. The command used was: graphmap align -Z -t 1 -r Ce_july12_2d.fasta -d dup.fq

Any ideas? Thanks James

Ce_july12_2d.fasta.gz

isovic commented 7 years ago

Hi James, Thank you for reporting this! Let me look into it and report back. The data will be very helpful! Best regards, Ivan.