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maickrau / GraphAligner

MIT License
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gaf format error in some case #74

Closed zhangyixing3 closed 1 year ago

zhangyixing3 commented 1 year ago

Dear Mr/Mrs, I mapping HiFI data to pggb.gfa by GraphAligner. The parameter is GraphAligner -g pggb.gfa -f reads_all.fasta.gz -a mapping_pggb.gaf -x vg -t 30. I find mapping_pggb.gaf format is strange as below. QQ截图20230216132714 Finally, I found that the format error was caused by HIFI data. Could you fix this problem in the future?

QQ截图20230216133203

Thank you very much .

maickrau commented 1 year ago

GraphAligner keeps the read name as is in the output. I'd recommend filtering the tags out of the input fasta with eg. cut -f 1 < hifi.fa > hifi_no_tags.fa. In this case you can also remove the tags from the gaf afterwards with awk -F "\t" '{OFS="\t"}substr($2,1,5)!="rq:f:"{print;}substr($2,1,5)=="rq:f:"{$2=""; print $0;}' < mapping_pggb.gaf | sed 's/\t\t/\t/g' > mapping_pggb_no_tags.gaf

zhangyixing3 commented 1 year ago

Thank you for your help ! I have solved this problem.