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format_detection finds ubam for bgzipped fastq file #96

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yhoogstrate opened this issue Oct 9, 2018 · 0 comments
Open

format_detection finds ubam for bgzipped fastq file #96

yhoogstrate opened this issue Oct 9, 2018 · 0 comments
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@yhoogstrate
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Hi there,

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

At the following line:

&& static_cast<unsigned char>(magic_number.at(2)) == 2;

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

@natir natir self-assigned this Oct 10, 2018
@natir natir added the bug label Oct 10, 2018
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