feature request: option to move fastq comments to sam tags

[eboyden]

Hi, I was wondering if an option to move the fastq comment (everything after the first whitespace, including additional whitespaces) to a field in the output sam file could be added. If the fastq comments were properly formatted as tab-delimited sam tags, then this would result in a properly formatted sam file with all metadata preserved. This is similar functionality to the BWA MEM -C option, or the Bowtie2 --sam-append-comment option, and is useful for e.g. transferring UMI information from fastqs to sam files without relying on additional files and formatting steps. Thanks!

[smarco]

Sure, we will make our best to include this option on the next patch/release.

Thanks for the feature request.