Change read mode for parameter files

Parameter files in these scripts were previously open without using the
'U' mode.

This should fix #727
Fixes issue #711

Modifies the defaults as @gregcaporaso suggested so that if a depth is not passed it will use the deepest available. Updated the documentation in the script and library and added a test.
Fixed performance bug in make_otu_heatmap_html.py.

Also removed a lot of old commented-out code. Fixes #731.
Merge pull request #742 from jrrideout/issue_731

Fixed performance bug in make_otu_heatmap_html.py.
Merge pull request #736 from ElDeveloper/params_U

Change read mode for parameter files -- issue 727
Updated to address initial problems.
Merge pull request #741 from wdwvt1/issue_711

Fixes issue #711