Apparently, SGA needs the input fastq files to be encoded in Phred+33, and crashes otherwise, without MATAM catching the error.
We need to add in the README/manual that fastq files need to be encoded in Phred+33. And we probably should check at the beginning of MATAM that we indeed have the correct encoding as input. This can be done by sampling a few of the reads and checking against the ASCII table for characters specific to either Phred+33 or Phred+64.
Apparently, SGA needs the input fastq files to be encoded in Phred+33, and crashes otherwise, without MATAM catching the error.
We need to add in the README/manual that fastq files need to be encoded in Phred+33. And we probably should check at the beginning of MATAM that we indeed have the correct encoding as input. This can be done by sampling a few of the reads and checking against the ASCII table for characters specific to either Phred+33 or Phred+64.