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Old 12-16-2014, 02:41 PM   #90
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

By unique, do you mean "only matching that sequence" or "occurring in a unique position in that sequence"? The latter cannot be done, but the former can be controlled with the "ambig" flag that I forgot to document. It is similar to BBMap's ambig flag. This is the description (which will be present in the next release):

ambiguous=random    (ambig) Set behavior on ambiguously-mapped reads (with an
                    equal number of kmer matches to multiple sequences).
                         first:  Use the first best-matching sequence.
                         toss:   Consider unmapped.
                         random: Select one best-matching sequence randomly.
                         all:    Use all best-matching sequences.
So, the default is random. With BBMap the default is "first".
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