fix #1076 stderr not loaded, using option_parse.error instead
changes based on @jrrideout comments
fix #1076 making stylistic change requested
fix #1110 changed to say files are whitespace separated not tab separated
Merge pull request #1177 from teravest/issue1076

fix #1076 stderr not loaded, using option_parse.error instead
fix #1142 added documentation for the default case.  Output seen from sourt_otu_table.py -h
Merge pull request #1182 from teravest/issue1142

fix #1142 added documentation for the default case.  Output seen from so...

I feel compelled to make a style comment... :grin:
fix #1150 updated -h documentation
changes recommeded by @gregcaporasso
Ignore extra samples when performing sanity checks

Fixes #1120.
Fix filename extensions in alpha_diversity.py

When invoked in batch-processing mode, the output filenames will now have a .txt extension instead of .biom. Fixes #1147.
Erroneous error message in split_libraries_fastq

The option mentioned in the error message should be
  --barcode_read_fps
instead of
  --barcode_fps
Slight modification to text in log file, added percent of total seqs demultiplexed, added unit test for demultiplex_fasta.py
uclust picker handles filenames with multiple dots

Intermediate .uc files are now correctly named based on the input sequences filename, including the case where there are multiple dots in the filename.

Also updated QIIME codebase to use uclust.py in pycogent_backports/ (was previously only being used in assign_taxonomy.py).

Fixes #191.
Added explicit test for zero length output sequence when truncating reverse primer and modified unit tests
update add_alpha_to_mapping_file.py to address #969
update virtual box docs to address #969
update otu_category_significance.rst to address #969
update core_diversity_analysis.rst to address #969
provided api-level control over line color, and added dashed line for median pre to median post