Make denoise_wrapper work again after using the fancy existing_filepaths option parser, which broke the code.
Use 'existing_filepaths' option in denoiser.py
Establish working dir and prefix earlier in __call__
Fixed filepath in shotgun tutorial.
updated comment
Refactored summarize_taxa.py to use BIOM API.

Virtually no interface changes, but underneath the code has been mostly rewritten to use the BIOM API for binning/collapsing. This also brings BIOM taxon tables one step closer to being fully integrated into QIIME.

Also generally cleaned things up and added more unit tests.

This was necessary for #998.
Added more details to lower/upper percentage docs.
Added initial one-to-many support.

Currently doesn't respect the 1-M handling method specified by the user, but the tests pass!
Added support for 'first' and 'add' 1-M modes.
Added strict=True to collapse call.
Added absolute_abundance optional argument.
Added support for divide 1-M relationship mode.
Read mapping now handles one-to-many metadata.
Added get_first_metadata_entry.

make_otu_heatmap* scripts now work with 1-M data.
Updated more code to support new table format.
Updated ChangeLog and map_reads_to_reference docs.
Merge pull request #1070 from jrrideout/issue-998

Merged
Revert "Merge pull request #1070 from jrrideout/issue-998"

This reverts commit ed1099cd7ffeac35fb454cfc75482ba334a6d109, reversing
changes made to 7b0920bfe0c1555244598118396b96c563b1128f.
Merge pull request #1073 from jrrideout/revert_pull_request_#1070

Revert "Merge pull request #1070 from jrrideout/issue-998"
Correct documentation of --header_id_regex option to RTAX.