Pretty self-explanatory. Sam spec is here:
https://samtools.github.io/hts-specs/SAMv1.pdf
All paired read alignments output paired reads together so adding the GO:query field to the @HD header line would be very helpful, since several downstream tools (e.g. fgbio ClipBam) require this explicitly, and it's inefficient to either modify the header directly or sort the already acceptably sorted file just to modify the header. Other aligners (bowtie2, bwa, minibwa, minimap2) have done this.
Pretty self-explanatory. Sam spec is here:
https://samtools.github.io/hts-specs/SAMv1.pdf
All paired read alignments output paired reads together so adding the
GO:queryfield to the@HDheader line would be very helpful, since several downstream tools (e.g. fgbio ClipBam) require this explicitly, and it's inefficient to either modify the header directly or sort the already acceptably sorted file just to modify the header. Other aligners (bowtie2, bwa, minibwa, minimap2) have done this.