The manual should explain what is encoded in the headers of output reads.

[cerebis]

PhageFilter/src/result_map.rs

Lines 32 to 45 in 9630952

	pub fn get_ext_id(&self, read_id: &String) -> String {
	let genomes = self
	.read_map
	.get(read_id)
	.map(|genome_set| {
	genome_set
	.iter()
	.map(AsRef::as_ref)
	.collect::<Vec<&str>>()
	.join(",")
	})
	.unwrap_or_default();
	read_id.clone() + " |" + &genomes
	}

The header appears to contain references to mapped genomes, but I do not see this explained in the documentation.

Is it possible to supply a ranking/score for each map? This is perhaps an ignorant question, as I do not know what is returned from searching the gSBT.

[Dreycey]

@cerebis - This a good point! I will work on ensuring there is documentation describing the headers for the sequences. The goal for adding these was to allow for extracting sequences corresponding to a particular species for downstream assembly if desired. That said, a score could be assigned next to each name corresponding to the degree of overlap. I think this would be a great feature to add - I'm going to add it as an agenda item