Changing Fastq header format #42
Description
I was speaking to Nuno at the Expression Atlas who said our format for Fastq headers is not compatible with CASAVA standard.
I think it would make sense to change the header format to one similar to described here: https://github.com/nunofonseca/fastq_utils
The biggest difference is that keeping the original read name at the end rather than beginning will make the read follow the CASAVA standard, but also some optimisations using the htslib API would be possible when parsing the header.
This would also allow us to use the fastq_utils script as an optional faster way to transform fastq files in protocols with simpler read topologies not requiring regular expressions (which are the majority of them).