misplaced bracket
fixed indel plots to handle huge datasets; also won't take hours; changed pipeline.py to comment out qualimap, fastqc and consensus until we can figure out the problems - this pipeline should finish without errors
Formats and copies cns.fq to readFastqFiles
Only samples from original experimental read files
changed % to percent
changed % to percent
updated summary plots a bit
Merge branch 'master' of https://github.com/mitenjain/nanopore
indel.py was writing to xml twice; commented out saving tmp.csv to output dir in favor of local temp dir
Doesn't copy empty cns.fq's to readFastqFiles
Reverting to old Consensus, no copy to readFiles
added regex to channel mappability in case fastq is not in correct format
small changes to cosmetics of coverage summary plots
small changes to cosmetics of coverage summary plots
more cosmetic improvements to various plots
fixed some stuff in kmer analysis; currently set to write all files to output for future debugging
added new meta analysis - kmer analysis of all unmapped reads. Also cleaned up regular kmer analysis. Should I do meta kmer analysis of reads that map as well?
forgot to add the new meta analysis to the pipeline.py that is on the master
Fix.
Merge remote-tracking branch 'origin/master' into em

Conflicts:
	nanopore/pipeline.py