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