printing duplicate (I think) lines

[jwasmuth]

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]

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