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smarco / gem3-mapper

GEM-Mapper v3
GNU General Public License v3.0
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feature request: option to move fastq comments to sam tags #30

Open eboyden opened 2 years ago

eboyden commented 2 years ago

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 commented 2 years ago

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

Thanks for the feature request.