map_barcodes: fixed confusing docstring

the sample barcode file was out of order
gitignore: user.cfg is ignored
check_barcodes: fixed the header
check_barcodes: added test & tools module
check_barcodes: logging sample names, not codes
rev comp barcode: added tests

and moved from Bio.Seq objects to just strings
tests: fixed an error in script call
util_index: moved common functions here

out of uc2otus and index_to_seq_table
test: refactored index tests
remove primers: refactored, added check tool

* Primer removal tests refactored into new file
* Primer removal module refactored into new util
* Tool to check for primer success added
tool: improved get tax tool
tools: count_mistmatches
tools: get_tax improved for uc files
tools: get_tax fixed typo
tools: tax audit
tools: improved/fixed tax audit
tax audit: top match
gg tax: improved
gg tax: improved message
check fastq: allow ambiguous formats to proceed

i had some fastq files that had ambiguous quality scores. rather than
stall the whole pipeline, it should just proceed anyway!