e4e7d39e2c
Problem: The sequence graphs can get very complex and it's not enough just to test that any given read has non-unique kmers. Reads with variants can have kmers that match unique regions of the reference, and this causes cycles in the final sequence graph. Ultimately the problem is that kmers of 10/25 may not be large enough for these complex regions. Solution: We continue to try kmers of 10/25 but detect whether cycles exist; if so, we do not use them. If (and only if) we can't get usable graphs from the 10/25 kmers, then we start iterating over larger kmers until we either can generate a graph without cycles or attempt too many iterations. |
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| src/org/broadinstitute/sting | ||
| test/org/broadinstitute/sting | ||