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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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Empty lines in Sam file #33

Closed mjpdejong closed 7 years ago

mjpdejong commented 7 years ago

Graphmap alignment resulted in a Sam-file containing emtpy lines. Downstream applications like samtools gave me errors because of this.

Case - Aligning of a 1D NanoPore E.Coli dataset to the reference genome

graphmap align \
        -t 32 \
        -C \
        -r U00096.2.fasta \
        -d $inputfile \
        -o /mnt/output/output.sam

Workaround I used, but not ideal: sed '/^$/d' output.sam > output.new.sam

isovic commented 7 years ago

Hi, thank you for reporting this! It should be fixed now. Best regards, Ivan.