A given read could have multiple passing alignments against different references. We either report those of as a CSV string, or collapse to lineage and report those hits (if still ambiguous) as a CSV string. We should implement some type of max-hits-to-report flag in the library def (or other spot TBD). If a given final reference combination has more reference than this threshold, those reads are simply stored as not matching. Or we could make a new category for 'Multi-Ref' or something.
We should apply this filter after lineage-coalescing, if that option is being used.
Examples:
max-hits-to-report' = 5
raw hit = alleles A, B, C, D, G, H, R
collapsing on lineage not selected
initial call: A,B,C,D,G,H,R
number of hits is 7, which is greater than 5, so this reference is filtered
max-hits-to-report' = 5
raw hit = Lineage1-AlleleA, Lineage1-AlleleB, Lineage1-AlleleC, Lineage2-AlleleD, Lineage2-AlleleG, Lineage2-AlleleF
collapsing on lineage is used.
initial call: Lineage1,Lineage2
number of hits is 2, so is allowed even though 7 raw alleles were matched
A given read could have multiple passing alignments against different references. We either report those of as a CSV string, or collapse to lineage and report those hits (if still ambiguous) as a CSV string. We should implement some type of max-hits-to-report flag in the library def (or other spot TBD). If a given final reference combination has more reference than this threshold, those reads are simply stored as not matching. Or we could make a new category for 'Multi-Ref' or something.
We should apply this filter after lineage-coalescing, if that option is being used.
Examples:
max-hits-to-report' = 5 raw hit = alleles A, B, C, D, G, H, R collapsing on lineage not selected initial call: A,B,C,D,G,H,R number of hits is 7, which is greater than 5, so this reference is filtered
max-hits-to-report' = 5 raw hit = Lineage1-AlleleA, Lineage1-AlleleB, Lineage1-AlleleC, Lineage2-AlleleD, Lineage2-AlleleG, Lineage2-AlleleF collapsing on lineage is used. initial call: Lineage1,Lineage2 number of hits is 2, so is allowed even though 7 raw alleles were matched