PRINSEQ bug - cannot deal with quality lines starting with @

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Roni Cohen-Fultheim

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Dec 23, 2020, 4:53:41 AM12/23/20

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Hello,

I have a FASTQ file with records such as the following:

@SRR5088880.sra.60846762 HWI:1:X:2:2216:6313:101073 length=50

TGCATGGTTCTGGGAAGGTTAAAATGGGCGGTGGGTGTCAGGCGCAGTGG

@?@?DBDD>CDFBHAEH?BFHIIIIIIGFGI)70@<@FGG9DCE><???A

unfortunately, it seems that due to the quality line beggining in @ the program expects the nextline to be a sequence (but of course it's another read name). Please advise.

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