initial code for finding likely location of sequencing errors in shotgun data
initial calc-error-profile code working
fixed up error profile calculation
fixed failing test to ignore first k bases in read in error profile
comment update; change default C for calc-error-profile
Merge branch 'reservoir_sampling' into kmer_error_profile
Merge branch 'master' of github.com:ged-lab/khmer into kmer_error_profile
cleanup of calc-error-profile
Merge branch 'master' of github.com:ged-lab/khmer into kmer_error_profile

Conflicts:
	tests/test_counting_hash.py
fixed +x for calc_error_profile
 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
clean up trim-low-abund & add location for temp files
script for collecting variant reads, using graphalign
Merge branch 'update/streaming' into feature/collect-variants
quick & dirty streaming error correction
correct-errors script cleanup
minor refactor of correct errors
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.