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
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'
Merge pull request #1730 from ElDeveloper/issue-1713

BUG: Update summarize_otu_by_cat.py to use biom 2.x
Merge branch 'master' of https://github.com/biocore/qiime into fix_1737

merging from upstream