README

March 4, 2016: 
	changed code to aggregate indels inside the mapping script
	changed format of indel track file to wig style to reduce size
	
	added convenience script to dump original fasta from region
	adding right shifts of indel calls during mapping to ensure 'easy' indel calls in homopolymers

...
March 28, 2016
	no realignment step - now flagging and reassembling the original set of reads
	skip alignment are flagged in addition to indels
March 29, 2016
	added graph spanning from tail to head in addition to head to tail for non-spanning graphs
	removal of poorly supported edges
March 30, 2016
	reads are kept in memory to be able to attempt adaptive k-mer size implementation
April 29, 2016
	keep track of skip flags separately from indel flags, try to use read id info to adjust active region boundaries
May 6, 2016
	added version of de Bruijn graph script to assemble reads with unknown orientation
	added flag to use that same script to do assembly from anchored reads and non-anchored ones
	reduced coverage stringency to retain precious reads spanning RE site
May 21, 2016
	dump and igv process preliminary reconstruction
	list of sam files rather than a single sam file
	add reference as a read. Accept high-confidence reconstruction if supported by at least one read and reference and low-confidence if one read (?)
	keep track in map of the nucleotide seen in the reference
	print basic stats for output including contig N50
May 22, 2016
	gaps dumped from local reference
	adjust notation and scripts to allow proper handling of local reference with different region flag trigger modes
May 23, 2016
	added stand-alone scripts to generate chain files and liftover bed annotations. Does not seem to be as useful as I hoped for
May 24, 2016
	commented out liftover track in reconstruction
	
	
June 11, 2016
	starting adapting to uger and slurm clusters
June 14, 2016
	changed preliminary set to do indexing together with length analysis
	indexing for partitioned fasta added
	TODO: now needs absolute paths, edit so that can take relative paths to multiple files
	
Oct, 2017
	rewrote in global positioning system, gnu parallel multithreading in favor of cluster management 
	
Nov 20, 2017
	added clip filtering
	trying weighted mapq
	command log print