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format_detection finds `ubam` for bgzipped fastq file

Open yhoogstrate opened this issue 5 years ago • 0 comments

Hi there,

I found a small error in the format detection that marks a bgzipped fastq as unaligned bam.

At the following line: https://github.com/labsquare/FastQt/blob/07da1bec97e50d2dcb3fbe77eaa0e0352a0b7a2e/utils/format_detection.cpp#L140 There needs to be an additional constraint that parses (using zlibs gzread or the included quagzipfile.h) the first 4 bases from the bgzipped file and ensures it equals [B][A][M][\1]

kind regards,

Youri

yhoogstrate avatar Oct 09 '18 09:10 yhoogstrate