From: Fred L. <fl...@sd...> - 2011-12-06 02:51:49
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I'm confused about how the newly defined "B" operator works. If it only backtracks in the query, then how do we get any overlapping bases or qual scores in the alignment? Can you show an example alignment? Thanks, FL > Hi Tim and Alec, > > After brief email exchanges with someone from CG, I realized that they are defining backward with respect to the _query_ sequence, instead of to the reference as I was originally proposing. And the more I think about it, the more I feel CG is taking the right route. When 'B' is for moving backward on the query, we naturally disallow a CIGAR like 50M1000B20M. In addition, CG should always produce CIGAR consistent in a backward overlap because it is taking the 4 subreads as a single unit when doing the alignment. Demanding consistent CIGAR in backward overlaps is a reasonable requirement which also simplifies implementation. |