Revision 5712 is the version prior to adding alleles.py and adding
left justification to atacAssembly.py

Format of output from Wayne's atac-indels.pl perl script (I call it indels.txt):

	0 FASTA sequence ID of first assembly (contig)
	1 Position number of start of first part of contig match
	2 Position number of end of first part of contig match
	3 Position number of start of second part of contig match
	4 Position number of end of second part of contig match
	5 Direction of first part of contig match (always 1)
	6 Direction of second part of contig match (always 1)
	7 FASTA sequence ID of second assembly (reference)
	8 Position number of start of first part of reference match
	9 Position number of end of first part of reference match
	10 Position number of start of second part of reference match
	11 Position number of end of second part of reference match
	12 Direction of first part of reference match
	13 Direction of second part of reference match (should be same as previous one)
	14 Gap between first and second parts of contig match
	15 Gap between first and second parts of reference match multiplied
				  by direction
Sort this file  by chromosome number with (8th field is fasta sequence id of
reference, i.e. chromosone number):
	cat indels.txt | sort -k 8,8 > indels.txt.sorted

To run indel finder you need:
	- .contig file from the soap run
	- the .atac.uids file from the atac run 

	from a writable directory, run:
		atacIndels.sh <reference_dir> <atac.uids_file> <contig_file>