Fix problem with plot_semivariogram.py

This is a quick fix for the fact that plot_semivariogram.py would fail
when the inputed mapping file contains more categories than the ones in
the distance matrix.

Fixes #1378
Addressing comments
Addressing comments
Merge branch 'master' of https://github.com/qiime/qiime into join_pair_one_file
Merge branch 'master' of github.com:antgonza/qiime into join_pair_one_file
Merge branch 'master' of https://github.com/qiime/qiime into join_pair_one_file
Merge branch 'master' of https://github.com/qiime/qiime into join_pair_one_file
Modified split_libraries.py to handle case of not finding a reverse primer (with truncate_remove option) and a low quality window, which was causing an error. This is to address issue #1336
Merge branch 'master' of https://github.com/qiime/qiime into join_pair_one_file
addressing @gregcaporaso comments
BUG: Update summarize_otu_by_cat.py to BIOM 2.x

This one slipped through the cracks, I have added an extra script usage
case to test for this.

Fixes #1713
Allows group_signifigance to skip rows

if a group row would cause an error in kruskal wallis, the p_val and
test stat are returned as nan
Merge pull request #1701 from walterst/split_libraries_issue1336

Modified split_libraries.py to handle case of not finding a reverse prim...
Merge pull request #1365 from antgonza/join_pair_one_file

Join pair ends from one file
DOC: Fix documentation problems
BUG: 'observation' -> 'sample'
MAINT/ENH: fixes #1201 and adds taxonomic assignment results to index page
MAINT: fixes #1292
MAINT: fixes #1339
MAINT: fixes #1352