Changes to be committed:
	modified:   scripts/abundance-dist-single.py
	modified:   scripts/abundance-dist.py
	modified:   scripts/count-median.py
	modified:   scripts/count-overlap.py
	modified:   scripts/extract-long-sequences.py
	modified:   scripts/extract-paired-reads.py
	modified:   scripts/fastq-to-fasta.py
	modified:   scripts/filter-abund-single.py
	modified:   scripts/interleave-reads.py
	modified:   scripts/load-graph.py
	modified:   scripts/load-into-counting.py
	modified:   scripts/make-initial-stoptags.py
	modified:   scripts/merge-partitions.py
	modified:   scripts/partition-graph.py
	modified:   scripts/split-paired-reads.py

scripts that WERE updated && notes:

abundance-dist			already does earlier in script
abundance-dist-single		already does earlier in script
count-overlap
extract-long-sequences
extract-paried-reads 		explicitly two output files; listed on one line:
				print('wrote to: ' + outfile + '.se' + ' and ' + outfile + '.pe')
fastq-to-fasta			file output optional; either outputs 'wrote to' message or 'did not write output to file'
filter-abund-single		already does earlier in script
interleave-reads		file output optional; either outputs 'wrote to' message or 'did not write output to file'
load-graph
load-into-counting		creates various partway files, messages for them already exists.
				'wrote to: ' message only prints on successful program end to ensure being printed
				at the end of output.
make-initial-stoptags		uncertain how output is written since script uses "htable.save_stop_tags()" instead
				of explicit file write object. 'wrote out: ' message added anyway.
merge-partitions		No API entry exists for this script!
				Already messages earlier in script
partition-graph			threading is confusing; potentially multiple files
split-paired-reads		explicitly two output files; message is:
				"'wrote to: ' + out1 + ' and ' + out2"

scripts that were NOT updated && notes on why:

annotate-partitions 		already does, multiple files
count-median 			already does
do-partition 			already does, multiple files
extract-paritions		already does, multiple files
filter-abund			already does, multiple files
filter-stoptags			already does, multiple files
find-knots			already does (mostly), multiple files, renames some things without outputting message
normalize-by-median		personally uncertain about logic flow && script appears to warn on output anyway
sample-reads-randomly		already does, multiple files
refactored scripts/fastq-to-fasta.py as per CTB instructions; set write_out to sys.stdout by default and cleaned up output file listing
Removed redundant file listings. Adjusted spacing.
fixed broken interleave-reads.py testing; now detects if outputting to file or stdout and lists as such.
fixed induced brokenness to fastq-to-fasta due to inattention in editor management.
Adjusted formatting to comply to pep8 standards.
Updated changelog to reflect earlier changes
Attempting to resolve optional file issue; primarily commiting to get Jenkins to test.
Fixed interleave-reads.py's optional file issue.
updated load-graph.py output listing to list all files written to. Also updated print statement to write to sys.stderr and to conform to python2 format.
Syntax is a learning experience.
:Fixed Changelog Conflicts.
c++11
Revert "c++11"

This reverts commit a4991cf652f6d27960a912183d3d57502f48354b.
Update executable bits
Address cppcheck warnings/errors not related to copy constructors; some false positives ignored
Run astyle on all cc/hh files in lib

Moved suppressions to inline comments, update Makefile accordingly and remove unused suppressions.txt

Fix assign_partition_id to use .empty() instead of .size()

Move cppcheck suppressions to same line as variables

Fix suppressions comment format, properly wrap nbfilled in ifdef
Fix indentation/run astyle
Added test for scripts/make-initial-stoptags.py
Updated output file listing to write to sys.stderr (imported sys as well)
Generated files for testing
Fixed formatting errors
Changed output listing print statements to print to sys.stderr
added test for #361, indent problem in script