Addressed a filtering issue introduced between QIIME 1.7 and 1.8

Originally spotted by [Zackary Jones](https://groups.google.com/forum/#!topic/qiime-forum/BojBxPn80Eo), this bug was due to the order in which filters are applied. If a precomputed mask is provided (e.g., the Lane mask), then it must be applied _before_ a gap filter. However, if an inferred mask is determined, it must be applied _after_ a gap filter.