Reducing complex methods

~~Please do not merge yet.~~

Working on reducing the complexity of some of the higher scoring methods in QIIME. Specifically:

```bash
(python27)16:23:35 qiime@master$ radon cc -s -n E qiime
qiime/filter_alignment.py
    F 61:0 apply_lane_mask_and_gap_filter - E (34)
qiime/make_3d_plots.py
    F 194:0 make_mage_output - E (40)
qiime/make_rarefaction_plots.py
    F 428:0 make_averages - F (48)
qiime/plot_taxa_summary.py
    F 856:0 get_counts - E (33)
qiime/split_libraries.py
    F 549:0 check_seqs - F (62)
    F 1146:0 preprocess - E (35)
qiime/workflow/core_diversity_analyses.py
    F 91:0 run_core_diversity_analyses - E (36)
qiime/workflow/upstream.py
    F 23:0 run_pick_de_novo_otus - E (36)
qiime/pycogent_backports/alpha_diversity.py
    F 863:0 ul_confidence_bounds - F (60)