and this is because it is reading the gzip-compressed FASTQ as if it was a normal FASTQ file. I'm not 100% sure but I believe FastQC runs normally when this set of parameters is used, so falco must behave similarly.
We can probably be able to figure out if it's compressed or not prior to processing, probably use igzfstream from smithlab_cpp would be the best option.
and this is because it is reading the gzip-compressed FASTQ as if it was a normal FASTQ file. I'm not 100% sure but I believe FastQC runs normally when this set of parameters is used, so falco must behave similarly.
We can probably be able to figure out if it's compressed or not prior to processing, probably use
igzfstreamfromsmithlab_cppwould be the best option.